VarScan mpileup to snp seems to be missing a call
the mpileup file looks like this...
Then, I'm using the following options in VarScan
And this is the line in the VCF where the problem is...
Attached is an image from IVG of the two alignments (front to back replicates of the same specimen, variant is clearly in both, but not in VCF)
Any thoughts? Apologies is the answer is obvious, but I can't seem to figure it out.
Thanks in advance
the mpileup file looks like this...
Code:
chr5 13894894 T 40 .a.AAAAAaAA,aaaaA,,aAA,AaaAaAaAaAAa,.,., B02/8/0///0G/3/10GH///C/5//0511//10HHH3A 55 a,....Aa,.AAa,aAAA.a,,,,...,,a..,,A,.,.,AaAAaA.aaA.,,,a !DHHHH0/HH1//H////G/HHGHHGFHH/GGHH/HHHFC////1/G/00FHHH)
Code:
mpileup2snp --min-coverage 20 --min-var-freq 0.2 --min-reads2 4 --strand-filter 1 --output-vcf 1 >whatever.vcf
Code:
chr5 13894894 . T A . PASS ADP=32;WT=1;HET=2;HOM=0;NC=1 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:53:40:25:11:14:56%:4.7528E-6:33:16:4:7:7:7 0/0:32:55:37:32:5:13.51%:2.706E-2:38:15:15:17:3:2
Any thoughts? Apologies is the answer is obvious, but I can't seem to figure it out.
Thanks in advance
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