count reference and alllele frequency from exome-seq bam

Question

[Chirag Nepal]

Hi all,

I have a bed file (list of SNPs of my interest).

I want to count the number of reads with mapping the reference sequence and variant sequence. Any suggestion on, which tools to use to retrieve this info?

Different predictions tools like varscan, somaticSnipper have reported such number, but the number slightly varies. If possible, can this be done with GATK or sam/bamtools.

Thanks in advance !

cheers

PS: I added the answer, below.

Answer 1

[poisonAlien]

Look at bam-readcount program.

Answer 2

[Ram]

GATK's DepthPerAlleleBySample annotation seems to do what you're asking for, though it works on VCF and not on BAM. Not sure if what you want can be done before variant calling.

Answer 3

[Chirag Nepal]

I found the way to count reads of both allele using varscan

java -jar VarScan.v2.3.7.jar readcounts mpileupFile --variants-file Test1 --output-file Test1Out

chrom    position    ref_base    depth    q20_depth    base:reads:strands:avg_qual:map_qual:plus_reads:minus_reads

chr1    982994    T    130    110    T:107:2:36:16:56:51:0    C:3:2:21:16:1:2    
chr1    1147297    G    23    22    G:18:2:35:17:9:9:0    A:4:1:33:17:4:0