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.
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written
by
Chirag Nepal
3 answers
Look at bam-readcount program.
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written
by
poisonAlien
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.
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
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