De novo mutations in cholinergic nicotinc receptor alpha 4 (chrna4) gene located on chromosome 20 (chr20: 63,343,310..63,375,471) of a progeny (NA12878) will be determined using the genomic information of parents (NA12891-Father and NA12892-Mother). This process needs a ped file as shown below.
This process involves 4 broader steps.
A. Process the sequencing files and generate base recalibrated BAM files
B. Call haplotypes using GATK HaplotypeCaller and recalibrate variants if applicable
C. Calculate genotype posterior likelihoods for given panel data and check for de novo mutation (in SNPs and INDELs)
D. Annotate variants (SNPs and INDELs)
E. Predict variant effect
Google Cloud Platform (GCP), 4 vCPUs, 15 GB RAM
Google Cloud Platform (GCP), 8 vCPUs, 30 GB RAM
Google Cloud Platform (GCP), 24 vCPUs, 32 GB RAM
AWS: c5.18xlarge (72 vCPUs, 144 GB RAM)
AWS: m5.24xlarge (96 vCPUs, 384 GiB RAM)
-The genome or a chromosomal region or a gene of interest of three individuals (NA12891, NA12892 and NA12878) will be analyzed.
-The genome sequencing data will be obtained from the 1000 genome project (http://www.internationalgenome.org/1000-genomes-browsers/)
-rw-rw-r-- 1 ubuntu ubuntu 66771360285 Apr 30 15:38 SRR622458_1.fastq.gz
-rw-rw-r-- 1 ubuntu ubuntu 68300205647 Apr 30 15:45 SRR622458_2.fastq.gz
-rw-rw-r-- 1 ubuntu ubuntu 68029335546 Apr 30 15:50 SRR622459_1.fastq.gz
-rw-rw-r-- 1 ubuntu ubuntu 69219443789 Apr 30 15:54 SRR622459_2.fastq.gz
-rw-rw-r-- 1 ubuntu ubuntu 4598249219 Apr 30 15:45 SRR622461_1.fastq.gz
-rw-rw-r-- 1 ubuntu ubuntu 4792383631 Apr 30 15:47 SRR622461_2.fastq.gz
@SRR622458.1 1/1
TGGGATTGGGGTAGGGCTAGGGCTCGGGTTGGGGATAGGGTGAGGGTTTGGGATAGGGGTAGGGTTAGGGTGTTGGCTAGGGTTAGGGCGAGGGCCAGGGC
@SRR622458.1 1/2
ATAACCCTAACCCTAACCCTAACGCTAACCCTAACCCTAACCCTAACCCTAACAATAACCCTAACCCTAACACTAACCTTACCCCTAACCCTAACCCTCAC
@SRR622459.1 1/1
GTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGAGATCGGAAG
@SRR622459.1 1/2
CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACAGATCGGAAG
@SRR622461.1 1/1
GCTAGGGGTAGGGTTAGGGCTCGGATTAGGGGTGGGATTAGGGTTAGAGGAAGTGATAGCCTTCAGGGTAGGGATCGGGCAAGGAATAGGATTGTGGGTGG
@SRR622461.1 1/2
ATAACCTAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACTCTATCACTGAACATAAGCCTTACCATACGTTCAAACATACA
~/gatk-data-ref$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta .
~/gatk-data-ref$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.dict .
~/gatk-data-ref$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai .
~/gatk-data-ref$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt .
~/gatk-data-ref$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb .
~/gatk-data-ref$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann .
~/gatk-data-ref$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt .
~/gatk-data-ref$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac .
~/gatk-data-ref$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa .
-rw-rw-r-- 1 ubuntu ubuntu 581712 Jan 6 2016 Homo_sapiens_assembly38.dict
-rw-rw-r-- 1 ubuntu ubuntu 3249912778 Jan 5 2016 Homo_sapiens_assembly38.fasta
-rw-rw-r-- 1 ubuntu ubuntu 160928 Dec 1 2016 Homo_sapiens_assembly38.fasta.fai
-rw-rw-r-- 1 ubuntu ubuntu 487553 Nov 6 23:47 Homo_sapiens_assembly38.fasta.64.alt
-rw-rw-r-- 1 ubuntu ubuntu 20199 Nov 6 23:47 Homo_sapiens_assembly38.fasta.64.amb
-rw-rw-r-- 1 ubuntu ubuntu 455474 Nov 6 23:47 Homo_sapiens_assembly38.fasta.64.ann
-rw-rw-r-- 1 ubuntu ubuntu 3217347004 Nov 6 23:47 Homo_sapiens_assembly38.fasta.64.bwt
-rw-rw-r-- 1 ubuntu ubuntu 804336731 Nov 6 23:48 Homo_sapiens_assembly38.fasta.64.pac
-rw-rw-r-- 1 ubuntu ubuntu 1608673512 Nov 6 23:48 Homo_sapiens_assembly38.fasta.64.sa
~/gatk-data-ref$ gsutil cp gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf dbsnp138.vcf
~/gatk-data-ref$ gsutil cp gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx dbsnp138.vcf.idx
~/gatk-data-ref$ gsutil cp gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz hg38.known_indels.vcf.gz
~/gatk-data-ref$ gsutil cp gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi hg38.known_indels.vcf.gz.tbi
~/gatk-data-ref$ gsutil cp gs://genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz gold_standard.indels.hg38.vcf.gz
~/gatk-data-ref$ gsutil cp gs://genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi gold_standard.indels.hg38.vcf.gz.tbi
-rw-rw-r-- 1 b0d2647 b0d2647 10950827213 May 6 02:45 dbsnp138.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 12480412 May 6 02:46 dbsnp138.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 20685880 May 6 02:48 gold_standard.indels.hg38.vcf.gz
-rw-rw-r-- 1 b0d2647 b0d2647 1500013 May 6 02:49 gold_standard.indels.hg38.vcf.gz.tbi
-rw-rw-r-- 1 b0d2647 b0d2647 61692306 May 6 02:46 hg38.known_indels.vcf.gz
-rw-rw-r-- 1 b0d2647 b0d2647 1567886 May 6 02:47 hg38.known_indels.vcf.gz.tbi
NA12891-Father
NA12892-Mother
NA12878-Daughter (progeny)
Alignment (bwa mem) will lead to a SAM (sequence alignment file) file, that will be converted to a BAM file (samtools view). It will be sorted (i.e., samtools sort) by co-ordinate and indexed (samtools index). Samtools flagstat will produce alignment statistics.
…………….
[main] Version: 0.7.17-r1188
…………………………..
[main] Real time: 27098.059 sec; CPU: 1337083.667 sec
[bam_sort_core] merging from 947 files and 1 in-memory blocks…
2448099046 + 0 in total (QC-passed reads + QC-failed reads)
11520983 + 0 secondary
12880297 + 0 supplementary
0 + 0 duplicates
2368472627 + 0 mapped (96.75% : N/A)
2423697766 + 0 paired in sequencing
1211848883 + 0 read1
1211848883 + 0 read2
2258885338 + 0 properly paired (93.20% : N/A)
2317266676 + 0 with itself and mate mapped
26804671 + 0 singletons (1.11% : N/A)
31022454 + 0 with mate mapped to a different chr
17456435 + 0 with mate mapped to a different chr (mapQ>=5)
-rw-rw-r– 1 b0d2647 b0d2647 189005777011 May 1 17:46 SRR622458.bam
-rw-rw-r– 1 b0d2647 b0d2647 9777672 May 1 19:12 SRR622458.bam.bai
……………
[Fri May 03 21:01:34 UTC 2019] picard.sam.ValidateSamFile done. Elapsed time: 443.41 minutes.
…………….
Tool returned: 3
## HISTOGRAM java.lang.String
Error Type Count
ERROR:INVALID_TAG_NM 207087
………………………
[Sun May 05 04:59:44 UTC 2019] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 684.96 minutes.
…………….
Tool returned: 0
……………….
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
P 26804671 1158633338 24401280 79626419 12149656 57133230 0 0.05393 11358780886
-rw-rw-r– 1 b0d2647 b0d2647 256414514748 May 4 05:07 SRR622458.fxNmMdUqTag.bam
-rw-rw-r– 1 b0d2647 b0d2647 9791560 May 4 17:18 SRR622458.fxNmMdUqTag.bam.bai
-rw-rw-r– 1 b0d2647 b0d2647 4604 May 5 04:59 SRR622458.fxNmMdUqTag.dupMetrics.txt
-rw-rw-r– 1 b0d2647 b0d2647 259148164965 May 5 04:59 SRR622458.fxNmMdUqTag.mdup.bam
05:17:58.920 INFO BaseRecalibrator - Writing recalibration report…
05:18:00.356 INFO BaseRecalibrator - …done!
05:18:00.356 INFO BaseRecalibrator - Shutting down engine
[May 7, 2019 5:18:00 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 888.11 minutes.
Runtime.totalMemory()=675807232
Tool returned: 2,100,435,052
Using GATK jar /home/b0d2647/miniconda3/share/gatk4-4.1.2.0-0/gatk-package-4.1.2.0-local.jar
………………………..
01:41:21.287 INFO ProgressMeter - Traversal complete. Processed 2448099046 total reads in 971.3 minutes.
01:41:21.338 INFO ApplyBQSR - Shutting down engine
[May 8, 2019 1:41:21 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 971.33 minutes.
Runtime.totalMemory()=177209344
Using GATK jar /home/b0d2647/miniconda3/share/gatk4-4.1.2.0-0/gatk-package-4.1.2.0-local.jar
-rw-rw-r-- 1 b0d2647 b0d2647 862101 May 7 05:18 SRR622458.fxNmMdUqTag.mdup.chrall.recal.table
-rw-rw-r-- 1 b0d2647 b0d2647 9843088 May 8 01:41 SRR622458.fxNmMdUqTag.mdup.rcal.bai
-rw-rw-r-- 1 b0d2647 b0d2647 249336008342 May 8 01:41 SRR622458.fxNmMdUqTag.mdup.rcal.bam
Alignment (bwa mem) will lead to a SAM (sequence alignment file) file, that will be converted to a BAM file (samtools view).
[main] Version: 0.7.17-r1188
………………..
[main] Real time: 22680.497 sec; CPU: 1393622.442 sec
sambamba 0.6.9 by Artem Tarasov and Pjotr Prins (C) 2012-2019
2467570854 + 0 in total (QC-passed reads + QC-failed reads)
10585005 + 0 secondary
11607447 + 0 supplementary
0 + 0 duplicates
2364732708 + 0 mapped (95.83%:N/A)
2445378402 + 0 paired in sequencing
1222689201 + 0 read1
1222689201 + 0 read2
2254822518 + 0 properly paired (92.21%:N/A)
2313333564 + 0 with itself and mate mapped
29206692 + 0 singletons (1.19%:N/A)
27935066 + 0 with mate mapped to a different chr
16234878 + 0 with mate mapped to a different chr (mapQ>=5)
-rw-rw-r– 1 ubuntu ubuntu 200710884147 May 2 11:47 SRR622459_1.bam
-rw-rw-r– 1 ubuntu ubuntu 192007490886 May 2 13:42 SRR622459_1.sorted.bam
-rw-rw-r– 1 ubuntu ubuntu 9775584 May 2 14:05 SRR622459_1.sorted.bam.bai
[bam_sort_core] merging from 192 files and 96 in-memory blocks…
-rw-rw-r– 1 ubuntu ubuntu 192007490886 May 2 13:42 SRR622459_1.sorted.bam
-rw-rw-r– 1 ubuntu ubuntu 9775584 May 2 14:05 SRR622459_1.sorted.bam.bai
## HISTOGRAM java.lang.String
Error Type Count
ERROR:INVALID_TAG_NM 245,444
[Sat May 04 19:07:58 UTC 2019] picard.sam.ValidateSamFile done. Elapsed time: 331.75 minutes.
…………..
Tool returned: 0
No errors found
…………….
[Sun May 05 05:03:29 UTC 2019] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 680.30 minutes.
Runtime.totalMemory()=3481796608
Tool returned: 0
…………..
……………
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
Q 29206692 1156666782 22192452 102838146 14050105 58665347 0 0.056085 11013720153
-rw-rw-r-- 1 b0d2647 b0d2647 691071 May 5 05:03 59_1.fxNm.log
-rw-rw-r-- 1 b0d2647 b0d2647 260704633123 May 4 10:23 SRR622459_1.sorted.NmMdTqTgs.bam
-rw-rw-r-- 1 b0d2647 b0d2647 9786952 May 4 18:05 SRR622459_1.sorted.NmMdTqTgs.bam.bai
-rw-rw-r-- 1 b0d2647 b0d2647 5565 May 5 05:03 SRR622459_1.sorted.NmMdTqTgs.dupMetrics.txt
-rw-rw-r-- 1 b0d2647 b0d2647 263473284570 May 5 05:03 SRR622459_1.sorted.NmMdTqTgs.mdup.bam
-rw-rw-r-- 1 b0d2647 b0d2647 9817616 May 5 09:59 SRR622459_1.sorted.NmMdTqTgs.mdup.bam.bai
-rw-rw-r-- 1 b0d2647 b0d2647 16 May 4 19:07 summary-SRR622459_1.sorted.NmMdTqTgs
…………………
05:59:20.762 INFO BaseRecalibrator - Writing recalibration report…
05:59:21.815 INFO BaseRecalibrator - …done!
05:59:21.815 INFO BaseRecalibrator - Shutting down engine
[May 7, 2019 5:59:21 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 889.98 minutes.
Runtime.totalMemory()=918028288
Tool returned: 2100022215
Using GATK jar /home/b0d2647/miniconda3/share/gatk4-4.1.2.0-0/gatk-package-4.1.2.0-local.jar
…………………..
01:27:37.393 INFO ProgressMeter - unmapped 952.2 2467258000 2591020.3
01:27:41.426 INFO ApplyBQSR - No reads filtered by: WellformedReadFilter
01:27:41.427 INFO ProgressMeter - unmapped 952.3 2467570854 2591166.0
01:27:41.428 INFO ProgressMeter - Traversal complete. Processed 2467570854 total reads in 952.3 minutes.
01:27:41.491 INFO ApplyBQSR - Shutting down engine
[May 8, 2019 1:27:41 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 952.33 minutes.
Runtime.totalMemory()=1529348096
Using GATK jar /home/b0d2647/miniconda3/share/gatk4-4.1.2.0-0/gatk-package-4.1.2.0-local.jar
…………………
-rw-rw-r-- 1 b0d2647 b0d2647 862101 May 7 05:59 SRR622459_1.sorted.NmMdTqTgs.mdup.chrall.recal.table
-rw-rw-r-- 1 b0d2647 b0d2647 9857240 May 8 01:27 SRR622459_1.sorted.NmMdTqTgs.mdup.recal.bai
-rw-rw-r-- 1 b0d2647 b0d2647 247018319690 May 8 01:27 SRR622459_1.sorted.NmMdTqTgs.mdup.recal.bam
Alignment (bwa mem) will lead to a SAM (sequence alignment file) file, that will be duplicate marked using samblaster. The sam file will be converted to a BAM file (samtools view). The BAM file will be sorted, indexed and subjected to generate alignment statistics
………………..
samblaster: Version 0.1.24
samblaster: Inputting from stdin
samblaster: Outputting to stdout
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
[M::process] read 7128714 sequences (720000114 bp)…
……….
samblaster: Marked 7066698 of 92459454 (7.64%) read ids as duplicates using 1,464,472k memory in 2M15S(135.165S) CPU seconds and 34M15S(2055S) wall time.
………………….
[main] Version: 0.7.17-r1188
…………………
[main] Real time: 2054.506 sec; CPU: 86258.664 sec
[bam_sort_core] merging from 71 files and 1 in-memory blocks…
186434670 + 0 in total (QC-passed reads + QC-failed reads)
745422 + 0 secondary
770340 + 0 supplementary
14305380 + 0 duplicates
177372458 + 0 mapped (95.14% : N/A)
184918908 + 0 paired in sequencing
92459454 + 0 read1
92459454 + 0 read2
168640536 + 0 properly paired (91.20% : N/A)
173607304 + 0 with itself and mate mapped
2249392 + 0 singletons (1.22% : N/A)
1688796 + 0 with mate mapped to a different chr
819246 + 0 with mate mapped to a different chr (mapQ>=5)
-rw-rw-r– 1 ubuntu ubuntu 12932312543 Apr 30 17:29 SRR622461.bam
-rw-rw-r– 1 ubuntu ubuntu 5679424 Apr 30 17:31 SRR622461.bam.bai
…………
Tool returned: 3
## HISTOGRAM java.lang.String
Error Type Count
ERROR:INVALID_TAG_NM 16164
…………..
Tool returned: 0
No errors found
……………
## METRICS CLASS picard.sam.DuplicationMetrics
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
R 2249392 86803652 1515762 9062212 635818 7009234 0 0.083331 508154568
16:58:10.698 INFO BaseRecalibrator - Writing recalibration report…
16:58:12.531 INFO BaseRecalibrator - …done!
16:58:12.531 INFO BaseRecalibrator - Shutting down engine
[May 6, 2019 4:58:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 128.13 minutes.
Runtime.totalMemory()=2802843648
Tool returned: 153117281
Using GATK jar /home/b0d2647/miniconda3/share/gatk4-4.1.2.0-0/gatk-package-4.1.2.0-local.jar
………………….
00:05:53.874 INFO ProgressMeter - unmapped 75.6 186417000 2466147.6
00:05:54.072 INFO ApplyBQSR - No reads filtered by: WellformedReadFilter
00:05:54.072 INFO ProgressMeter - unmapped 75.6 186434670 2466273.1
00:05:54.073 INFO ProgressMeter - Traversal complete. Processed 186434670 total reads in 75.6 minutes.
00:05:54.124 INFO ApplyBQSR - Shutting down engine
[May 7, 2019 12:05:54 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 75.62 minutes.
Runtime.totalMemory()=394788864
Using GATK jar /home/b0d2647/miniconda3/share/gatk4-4.1.2.0-0/gatk-package-4.1.2.0-local.jar
-rw-rw-r-- 1 b0d2647 b0d2647 17553093573 May 6 04:00 SRR622461.fxNmMdUqTag.bam
-rw-rw-r-- 1 b0d2647 b0d2647 8846296 May 6 17:08 SRR622461.fxNmMdUqTag.bam.bai
-rw-rw-r-- 1 b0d2647 b0d2647 3531 May 6 14:42 SRR622461.fxNmMdUqTag.dupMetrics.txt
-rw-rw-r-- 1 b0d2647 b0d2647 17728293924 May 6 14:42 SRR622461.fxNmMdUqTag.mdup.bam
-rw-rw-r-- 1 b0d2647 b0d2647 8959264 May 6 17:08 SRR622461.fxNmMdUqTag.mdup.bam.bai
-rw-rw-r-- 1 b0d2647 b0d2647 854355 May 6 16:58 SRR622461.fxNmMdUqTag.mdup.chrall.recal.table
-rw-rw-r-- 1 b0d2647 b0d2647 9188048 May 7 00:05 SRR622461.fxNmMdUqTag.mdup.recal.bai
-rw-rw-r-- 1 b0d2647 b0d2647 20573738839 May 7 00:05 SRR622461.fxNmMdUqTag.mdup.recal.bam
-rw-rw-r-- 1 b0d2647 b0d2647 16 May 6 04:38 summary-SRR622461.fxNmMdUqTag
-rw-rw-r-- 1 b0d2647 b0d2647 124 May 8 03:25 NA128-78-91-92.ped
-rw-rw-r-- 1 b0d2647 b0d2647 205909 May 8 02:26 SRR6224-58-59-61.fxTgs.mdup.recal.chrna4.jcalls.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 118100 May 8 02:26 SRR6224-58-59-61.fxTgs.mdup.recal.chrna4.jcalls.vcf.idx
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR6224-58-59-61.fxTgs.mdup.recal.chrna4.jcalls.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR6224-58-59-61.fxTgs.mdup.recal.chrna4.jcalls.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 3
SN 0 number of records: 117
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 97
SN 0 number of MNPs: 0
SN 0 number of indels: 20
SN 0 number of others: 0
SN 0 number of multiallelic sites: 3
SN 0 number of multiallelic SNP sites: 2
This run needs a ped file whose structure is shown below:
FamID IndID PatID MatID Sex Phenotype
CEUTrio NA12891 0 0 1 0
CEUTrio NA12892 0 0 2 0
CEUTrio NA12878 NA12891 NA12892 2 0
-rw-rw-r-- 1 b0d2647 b0d2647 214598 May 8 03:29 SRR6224-58-59-61.fxTgs.mdup.recal.chrna4.jcalls.genoPosteriors.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 118115 May 8 03:29 SRR6224-58-59-61.fxTgs.mdup.recal.chrna4.jcalls.genoPosteriors.vcf.idx
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR6224-58-59-61.fxTgs.mdup.recal.chrna4.jcalls.genoPosteriors.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR6224-58-59-61.fxTgs.mdup.recal.chrna4.jcalls.genoPosteriors.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 3
SN 0 number of records: 117
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 97
SN 0 number of MNPs: 0
SN 0 number of indels: 20
SN 0 number of others: 0
SN 0 number of multiallelic sites: 3
SN 0 number of multiallelic SNP sites: 2
18:05:28.024 INFO ProgressMeter - Traversal complete. Processed 97 total variants in 0.0 minutes.
18:16:54.657 INFO ProgressMeter - Traversal complete. Processed 97 total variants in 0.0 minutes.
…………
18:40:22.548 INFO PedReader - Phenotype is other? true
18:40:22.696 INFO ProgressMeter - unmapped 0.0 97 24978.5
##INFO=<ID=hiConfDeNovo,Number=1,Type=String,Description="High confidence possible de novo mutation (GQ >= 20 for all trio members)=[comma-delimited list of child samples]">
##INFO=<ID=loConfDeNovo,Number=1,Type=String,Description="Low confidence possible de novo mutation (GQ >= 10 for child, GQ > 0 for parents)=[comma-delimited list of child samples]">
18:07:49.372 INFO ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
18:28:37.031 INFO ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes.
##INFO=<ID=hiConfDeNovo,Number=1,Type=String,Description="High confidence possible de novo mutation (GQ >= 20 for all trio members)=[comma-delimited list of child samples]">
##INFO=<ID=loConfDeNovo,Number=1,Type=String,Description="Low confidence possible de novo mutation (GQ >= 10 for child, GQ > 0 for parents)=[comma-delimited list of child samples]">
00:20:44.479 WARN VariantsToTable - Allele-specific fields will only be split if splitting multi-allelic variants is specified (--split-multi- allelic or -SMA
………….
00:20:44.515 INFO ProgressMeter - Traversal complete. Processed 20 total variants in 0.0 minutes. …………..
CHROM POS ID REF ALT TYPE
chr20 63344477 rs11480478 A AT INDEL
chr20 63344494 rs11480479 C CA INDEL
chr20 63353961 . C CGGTCCTGGGGGGTCTGT INDEL
chr20 63356992 rs71197409 C CGACCACATCGCCATG INDEL
chr20 63357155 rs147641999 GTCTCCACAGGACCACATTCCCACAGGACCACAACCCACAGGACCACA G INDEL
chr20 63357288 rs377681750 ACAGGACCTCATCCCCT A INDEL
chr20 63357664 rs3838009 CG C INDEL
chr20 63358946 rs11483065 T TC INDEL
chr20 63359022 rs59320601 CT C INDEL
chr20 63359045 rs11472833 G GGA INDEL
chr20 63359051 rs11478664 AT A INDEL
chr20 63359866 rs67528285 GCT G INDEL
chr20 63359884 rs11472697 T TGCGC INDEL
chr20 63359903 . G GTGTGTGTGTGCCGGGCGTGCGC,GTGTGTGTGTGTGTGCCGGGCGTGCGC INDEL
chr20 63359905 . G GTGTGTGTGTGTGCCGGGCGTGCGC INDEL
chr20 63361431 . G GGGAGGGGGAGGAGGGGGAGCAGTGGAGGGGGGAGAAGAGGAGGGGGGAGGA INDEL
chr20 63362320 rs5842418 G GC INDEL
chr20 63367151 rs61330515 CT C INDEL
chr20 63367164 rs35621466 TG T INDEL
chr20 63369500 rs141840462 CAG C INDEL
……………
23:49:09.135 INFO ProgressMeter - Traversal complete. Processed 97 total variants in 0.0 minutes.
…………..
CHROM POS ID REF ALT TYPE NA12878.AD NA12891.AD NA12892.AD
chr20 63346204 rs2236196 G A SNP 0,6 0,47 22,33
chr20 63347172 rs6090380 T C SNP 0,2 0,19 16,10
chr20 63347748 rs3787137 G A SNP 1,2 22,0 13,21
chr20 63347872 rs3787138 G A SNP 0,4 1,24 22,26
chr20 63348208 rs6062439 G C SNP 0,2 0,16 15,12
chr20 63348271 rs45486392 T C SNP 5,0 24,16 37,0
chr20 63348441 rs6062899 G A SNP 0,6 0,32 14,17
chr20 63348773 rs6062900 C T SNP 0,4 0,28 11,16
chr20 63348909 rs6062901 G A SNP NA 0,29 6,9
chr20 63349639 rs3827020 T C SNP 1,0 0,18 30,0
chr20 63349752 rs1044397 C T SNP NA 19,0 10,16
chr20 63349782 rs1044396 G A SNP NA 19,0 12,18
chr20 63350184 rs2229960 A G SNP 0,1 0,33 14,12
chr20 63350202 rs2229959 C A SNP 0,2 0,37 13,13
chr20 63350733 rs1044394 A G SNP 0,2 0,35 13,18
chr20 63350772 rs1044393 A G SNP 0,3 0,33 18,14
chr20 63351340 rs6011772 C T SNP 0,5 0,40 21,20
chr20 63351529 rs4809541 C T SNP 0,3 0,37 14,19
chr20 63351871 rs6090382 T C SNP 0,3 0,21 9,14
chr20 63351959 rs45577639 G A SNP 1,2 0,20 23,0
chr20 63352162 rs6011774 C T SNP 0,3 29,0 13,14
chr20 63352404 rs6011776 C T SNP 0,5 0,24 13,7
chr20 63352965 rs6011779 C T SNP 0,1 0,27 13,19
chr20 63353656 rs114300953 G A SNP 1,0 1,4 9,0
chr20 63353875 rs74213202 A T SNP 0,0 3,3 5,4
chr20 63353888 rs74201270 C G SNP 1,0 3,2 5,3
chr20 63353902 rs79514729 G A SNP NA 1,1 5,1
chr20 63353971 rs74177996 A G SNP NA 0,9 5,7
chr20 63354009 rs75898014 G T SNP NA 7,4 13,0
chr20 63356709 rs2273504 G A SNP 1,0 0,24 11,0
chr20 63357030 rs13036436 G A SNP 0,1 0,54 16,22
chr20 63357043 rs13042047 C T SNP 0,1 0,52 20,24
chr20 63357047 rs13040031 A T SNP 0,1 0,54 20,27
chr20 63357061 rs12479680 A G SNP 0,1 0,52 22,23
chr20 63358149 rs6010918 A G SNP 0,3 0,30 21,16
chr20 63359026 rs60207571 T C SNP 0,2 0,37 0,31
chr20 63359068 rs6011786 C A SNP 0,2 0,37 0,35
chr20 63359069 rs6011787 T C SNP 0,2 0,37 0,36
chr20 63359522 rs6090384 T C SNP 0,1 0,27 13,22
chr20 63359789 rs3818204 G A SNP NA 0,21 25,0
chr20 63359895 rs6011789 T C SNP 0,4 0,14 10,5
chr20 63359949 rs45457196 A C SNP 0,3 0,22 1,26
chr20 63360368 rs6090385 C A SNP 1,3 24,0 0,40
chr20 63360653 rs11697662 C T SNP 0,3 0,16 0,31
chr20 63360933 rs11698563 A C SNP 1,0 8,0 0,8
chr20 63361195 rs6090387 G C SNP NA 1,2 0,3
chr20 63361453 rs58134915 T A SNP 0,1 0,13 0,12
chr20 63361486 rs13043186 A G SNP 2,1 22,0 0,19
chr20 63361542 rs12624510 G A SNP 0,1 15,7 18,0
chr20 63361854 rs6122429 C T SNP 1,2 14,9 40,0
chr20 63361875 rs12625596 A C,G SNP 0,0,1 0,27,0 0,0,42
chr20 63362033 rs13044526 G A SNP 0,1 12,15 0,21
chr20 63362289 rs45474898 C T SNP 2,0 15,16 26,0
chr20 63362349 rs750263 T C SNP 0,2 0,30 0,22
chr20 63362361 rs13040954 C G SNP 2,0 8,18 22,0
chr20 63362406 rs911044 C T SNP 0,1 0,35 0,36
chr20 63362415 rs750264 C A,G SNP 0,0,2 0,13,18 0,0,31
chr20 63362438 rs7261696 A G SNP 2,0 15,18 39,0
chr20 63362590 rs2093107 A G SNP 2,0 12,14 0,20
chr20 63362601 rs7267689 G C SNP 2,0 14,15 21,0
chr20 63362912 rs755203 G A SNP 2,2 45,0 0,51
chr20 63363313 rs3810471 C T SNP 3,5 37,0 0,47
chr20 63363870 rs11086163 G C SNP 6,0 17,23 47,0
chr20 63363970 rs6011794 C T SNP 0,1 0,33 0,19
chr20 63365354 rs910895 A G SNP 0,1 13,14 0,27
chr20 63365549 rs7267923 A G SNP 2,6 40,0 0,35
chr20 63365935 rs6011796 C T SNP 0,1 0,26 0,37
chr20 63366209 rs4990923 A G SNP NA 1,5 2,3
chr20 63366229 rs2314696 A G SNP 0,1 1,15 0,18
chr20 63366549 rs62206949 T G SNP 5,0 22,23 36,1
chr20 63366616 rs11696339 G A SNP 2,0 17,21 0,38
chr20 63366732 rs62206950 A G SNP 0,3 0,21 0,32
chr20 63366800 rs62206951 C T SNP 1,0 16,13 22,0
chr20 63366822 rs72629023 G T SNP 1,0 13,17 26,0
chr20 63367091 rs6062905 T C SNP 0,2 0,17 0,25
chr20 63367956 rs6089899 G A SNP NA 23,0 0,21
chr20 63368317 rs4809295 T C SNP NA 0,30 0,32
chr20 63368417 rs6122430 G A SNP 2,3 14,17 34,0
chr20 63368803 rs911045 A G SNP 0,5 0,47 0,46
chr20 63368850 rs735501 T C SNP 4,0 25,30 53,0
chr20 63369260 rs911046 T C SNP 0,6 0,61 0,48
chr20 63369496 rs11086164 C T SNP 1,0 32,36 53,0
chr20 63370049 . G A SNP 3,0 26,0 12,18
chr20 63370155 rs6010919 C A SNP 1,0 11,23 28,0
chr20 63370156 rs6010920 G A SNP 1,0 11,23 28,0
chr20 63370194 rs1107953 C T SNP NA 28,19 0,28
chr20 63370757 rs4809549 G C SNP NA 15,29 0,30
chr20 63372095 rs60367095 A T SNP NA 18,23 31,0
chr20 63372140 rs57619853 T C SNP 1,0 17,21 28,0
chr20 63373587 rs34555947 G A SNP 1,0 21,0 11,15
chr20 63373634 rs34638379 C A SNP 2,0 27,0 17,20
chr20 63373693 rs34668034 C T SNP 2,0 26,0 22,20
chr20 63374106 rs35318934 G C SNP NA 36,0 13,16
chr20 63374286 rs6089900 C G SNP 5,0 34,0 19,16
chr20 63374536 rs7266872 G A SNP 3,0 16,17 51,0
https://useast.ensembl.org/info/docs/tools/vep/index.html
CHROM POS . REF ALT
chr20 63346204 . G A
chr20 63347172 . T C
chr20 63347748 . G A
chr20 63347872 . G A
chr20 63348208 . G C
chr20 63348271 . T C
chr20 63348441 . G A
chr20 63348773 . C T
chr20 63348909 . G A
vep_output
chrna4.snp <-read.table("91-92-78-chrna-snp.txt")
head(chrna4.snp)
chrna4.snp <-read.table("91-92-78-chrna-snp.txt")
str(chrna4.snp)
'data.frame': 1094 obs. of 38 variables:
$ V1 : Factor w/ 1 level ".": 1 1 1 1 1 1 1 1 1 1 ...
$ V2 : Factor w/ 95 levels "20:63346204-63346204",..: 1 1 1 1 1 1 1 1 1 1 ...
$ V3 : Factor w/ 4 levels "A","C","G","T": 1 1 1 1 1 1 1 1 1 1 ...
$ V4 : Factor w/ 13 levels "3_prime_UTR_variant",..: 1 9 5 5 1 5 5 5 9 5 ...
$ V5 : Factor w/ 2 levels "LOW","MODIFIER": 2 2 2 2 2 2 2 2 2 2 ...
$ V6 : Factor w/ 3 levels "-","AL121827.1",..: 3 3 3 3 3 3 3 3 3 3 ...
$ V7 : Factor w/ 3 levels "-","ENSG00000101204",..: 2 2 2 2 2 2 2 2 2 2 ...
$ V8 : Factor w/ 2 levels "RegulatoryFeature",..: 2 2 2 2 2 2 2 2 2 2 ...
$ V9 : Factor w/ 37 levels "ENSR00000657632",..: 17 19 20 23 24 26 29 30 31 35 ...
$ V10: Factor w/ 10 levels "antisense","CTCF_binding_site",..: 9 6 6 4 9 4 6 10 10 6 ...
$ V11: Factor w/ 14 levels "-","1/1","1/6",..: 12 10 1 1 14 1 1 1 2 1 ...
$ V12: Factor w/ 18 levels "-","1/1","1/2",..: 1 1 1 1 1 1 1 1 1 1 ...
$ V13: Factor w/ 1 level "-": 1 1 1 1 1 1 1 1 1 1 ...
$ V14: Factor w/ 1 level "-": 1 1 1 1 1 1 1 1 1 1 ...
$ V15: Factor w/ 72 levels "-","1009","110",..: 42 46 1 1 45 1 1 1 60 1 ...
$ V16: Factor w/ 13 levels "-","1014","1209",..: 1 1 1 1 1 1 1 1 1 1 ...
$ V17: Factor w/ 13 levels "-","142","155",..: 1 1 1 1 1 1 1 1 1 1 ...
$ V18: Factor w/ 6 levels "-","A","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
$ V19: Factor w/ 6 levels "-","agC/agT",..: 1 1 1 1 1 1 1 1 1 1 ...
$ V20: Factor w/ 95 levels "rs1044393","rs1044394",..: 24 24 24 24 24 24 24 24 24 24 ...
$ V21: Factor w/ 521 levels "-","1000","1002",..: 1 1 354 354 1 354 422 309 1 425 ...
$ V22: Factor w/ 3 levels "-","-1","1": 2 2 2 2 2 2 2 2 2 2 ...
$ V23: Factor w/ 2 levels "-","cds_start_NF": 1 1 1 2 1 1 1 1 1 1 ...
$ V24: Factor w/ 3 levels "-","Clone_based_ensembl_gene",..: 3 3 3 3 3 3 3 3 3 3 ...
$ V25: Factor w/ 2 levels "-","HGNC:1958": 2 2 2 2 2 2 2 2 2 2 ...
$ V26: Factor w/ 6 levels "-","1","2","3",..: 2 2 2 6 6 2 5 1 1 6 ...
$ V27: Factor w/ 2 levels "-","P1": 2 1 1 1 1 1 1 1 1 1 ...
$ V28: Factor w/ 1 level "-": 1 1 1 1 1 1 1 1 1 1 ...
$ V29: Factor w/ 1 level "-": 1 1 1 1 1 1 1 1 1 1 ...
$ V30: Factor w/ 69 levels "-","0.0010","0.0110",..: 1 1 1 1 1 1 1 1 1 1 ...
$ V31: Factor w/ 4 levels "-","benign","benign,protective",..: 1 1 1 1 1 1 1 1 1 1 ...
$ V32: Factor w/ 1 level "-": 1 1 1 1 1 1 1 1 1 1 ...
$ V33: Factor w/ 3 levels "-","0,1","1": 2 2 2 2 2 2 2 2 2 2 ...
$ V34: Factor w/ 26 levels "-","15154117,26102342",..: 22 22 22 22 22 22 22 22 22 22 ...
$ V35: Factor w/ 1 level "-": 1 1 1 1 1 1 1 1 1 1 ...
$ V36: Factor w/ 1 level "-": 1 1 1 1 1 1 1 1 1 1 ...
$ V37: Factor w/ 1 level "-": 1 1 1 1 1 1 1 1 1 1 ...
$ V38: Factor w/ 1 level "-": 1 1 1 1 1 1 1 1 1 1 ...