SAM/BAM: Annotation and analysis of next-generation sequencing data

SAM/BAM Documentation

Here is the documentation for SAM.

Below is snippet of a SAM file:

SAMsnippet

LINUX based tools

github-samtools

bioconda-samtools

github-bamtools

bioconda-bamtools

github-sambamba

bioconda-sambamba

LINUX commands for analysis of SAM file

number of alignments contained insertions

cat xxxxxx.sam | cut -f6|grep “I”|wc -l

number of alignments contained deletions

cat xxxxxx.sam | cut -f6|grep “D”|wc -l

number of alignments contained both insertions and deletions

cat xxxxxx.sam | cut -f6|grep “I”|grep “D”|wc -l

number of alignments contained insertions and/or deletions

cut -f6 xxxxxx.sam | grep -c “[I,D]”

total number of reads (including no. reads unpaired, non-aligned, aligned once or more than once)

samtools flagstat xxxxxx.sam

LINUX commands for analysis of BAM file

number of sequences in the file

samtools view -H xxxxxx.bam | grep -c “SN:”

Length of 1st sequence in the file

samtools view -H xxxxxx.bam | grep “SN:” | more

name of the alignment tool

samtools view -H xxxxxx.bam | grep “^@PG”

identifier (name) for the first alignment

samtools view xxxxxx.bam | head -1 | cut -f1

number of alignments in the file

samtools flagstat xxxxxx.bam

samtools view xxxxxx.bam | wc -l

number of unmapped reads

samtools view xxxxxx.bam | cut -f3 | grep -v ’*’ | wc -l

number of spliced alignments

samtools view xxxxxx.bam |cut -f6|grep “N”|wc -l

samtools view xxxxxx.bam | cut -f6 | grep -c ‘N’

number of alignments containing a deletion (D)

samtools view xxxxxx.bam| cut -f6|grep “D”|wc -l

samtools view xxxxxx.bam | cut -f6 | grep -c ‘D’

alignment with an unmapped mate (*)

samtools view xxxxxx.bam| cut -f7|grep “*“|wc -l

number of alignments where the read’s mate mapped to the same chromosome

samtools view xxxxxx.bam| cut -f7|grep “=”|wc -l

Data extraction from a defined chromosomal region: First, sort and index the file

samtools sort xxxxxx.bam xxxxxx.sorted.bam

samtools index xxxxxx.sorted.bam

number of alignments in a specified chromosomal region

samtools view xxxxxx.sorted.bam “Chr3:11777000-11794000”|wc -l

number of unmapped mates in a specified chromosomal region

samtools view xxxxxx.sorted.bam “Chr3:11777000-11794000”|cut -f7|grep “*“|wc -l

number of deletions in a specified chromosomal region

samtools view xxxxxx.sorted.bam “Chr3:11777000-11794000”|cut -f6|grep “D”|wc -l

number of mapped mates in a specified chromosomal region

samtools view xxxxxx.sorted.bam “Chr3:11777000-11794000”|cut -f7|grep “=”|wc -l

number of splicing in a specified chromosomal region

samtools view xxxxxx.sorted.bam “Chr3:11777000-11794000”|cut -f6|grep “N”|wc -l

An alternative approach to extract data from a particular chromosomal region

samtools view -b xxxxxx.sorted.bam “Chr3:11777000-11794000” > xxxxxx.region.bam

samtools flagstat xxxxxx.region.bam

samtools view xxxxxx.bam | cut -f6 | grep -c ‘N’

samtools view xxxxxx.region.bam | cut -f6 | grep -c ‘D’

samtools view xxxxxx.region.bam | cut -f7 | grep -c ’*’

samtools view xxxxxx.bam | cut -f7 | grep -c ‘=’