calculate the base distribution of a SAM/BAM file

[weberma]

Hi everyone,

I have BAM files and want to know the base distribution at a given reference position. Samtools view can give my all reads that overlap with the reference position but then I have to parse the cigar strings to get the corresponding base from the read. I tried to get the information from VCF/BCF generated by samtools mpileup but they doesn't contain what I am looking for.

Any suggestions?

Cheers,
Mathias

[aaronh]

samtools mpileup should give you what you need if you don't pass it to bcftools. Another way would be to load the bam file into IGV and get the summary there.

[pallevillesen]

mpileup

samtools mpileup -BQ0 -d100000 -f hg19.fa -r chr1:17420-17420 BAMFILE

Will give you the mpileup format for 1 position (then you must parse it). There is a number of parsers around - if you can't find one you can have mine (perl).

samtools mpileup -BQ0 -d100000 -f hg19.fa -l BEDFILE BAMFILE

Will do it for a file with one region/position pr. line

If you need parsing inspiration: https://github.com/riverlee/pileup2b...p2baseindel.pl

[weberma]

Thank you very much, this was exactly what I was looking for.