Question: count reference and alllele frequency from exome-seq bam
0
gravatar for Chirag Nepal
4.6 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

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.

allele-frequency variant exome • 1.4k views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Chirag Nepal2.2k
1
gravatar for poisonAlien
4.6 years ago by
poisonAlien2.8k
Asgard
poisonAlien2.8k wrote:

Look at bam-readcount programme.

ADD COMMENTlink written 4.6 years ago by poisonAlien2.8k
0
gravatar for RamRS
4.6 years ago by
RamRS24k
Houston, TX
RamRS24k wrote:

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.

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by RamRS24k
0
gravatar for Chirag Nepal
4.6 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

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   

 

 

ADD COMMENTlink written 4.6 years ago by Chirag Nepal2.2k
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