Pooled sample SNP calling: SNVer

[lung1212]

I am working on a pooled samples re-sequencing project. There are 10 pools for cases and controls respectively. I am calling SNV using SNVer, just wondering do I need to call SNV in cases and controls separately? do I can call them simutaneously?

[TiborNagy]

If you would like to compare cases with controls, you have to run it seperately.

[lung1212]

thanks a lot. but i think i encounter a problem, i called SNV separately , some rare SNV can be called in case pool, but showed NA in control pool, what does it mean....?

[TiborNagy]

Can you paste an NA record here? I have never seen NA in VCF file.

[lung1212]

##fileformat=VCFv4.0
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=.,Type=Float,Description="Alternative Allele Frequency">
##INFO=<ID=NP,Number=1,Type=Integer,Description="Number of Pools">
##INFO=<ID=PV,Number=.,Type=Float,Description="Pvalue generated by SNVer">
##FORMAT=<ID=AC,Number=1,Type=Integer,Description="Alternative Allele Count">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1P1 S1P10 S1P11 S1P12 S1P13 S1P14 S1P15 S1P16 S1P17 S1P18 S1P19 S1P2 S1P20 S1P21 S1P22 S1P23 S1P24 S1P3 S1P4 S1P5 S1P6 S1P7 S1P8 S1P9
chr1 1234567 . C T . PASS DP=13135;AF=0.005;NP=22;PV=2.4424906541753444E-15 ACP 0:598 0:518 0:259 62:594 NA:NA 0:462 0:627 0:579 0:427 0:652 0:543 0:645 0:594 0:410 0:402 0:407 0:313 0:590 0:547 0:820 NA:NA 0:570 0:587 0:721





BTW, our design is : 10 individuals a pool; targeted sequencing of a few regions; so around 20 pools were sequenced in a single lane. these 20 pools consist of both cases and controls.

So your suggestion is:
call cases and controls separately; do I need to call SNV base on lane as well?

[TiborNagy]

The NA means there is no coverage in those samples. I think you do not need to call SNVs per lane.