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Hi all.
SNVer is giving me a couple issues. Briefly, I set up a pileline utilizing Bowtie2, samtools sort/rmdup and SNVer for SNV calls. I have sample MySeq reads from Simian Immunodeficiancy Virus that map very well and call tons of low Pvalue variants with my pipeline. I have recently recieved new viral reads for a different project and no variants are called with the pipe. When I change from SNVer to samtools mpileup it calls 8 variants, which are all ~100% of the population. I have tried aligning with bwa as SNVer suggests with the same result.
*.raw.vcf file.
FMuLV_amp_trim 213 . c c . PASS DP=4987;AF=0.000;NP=1;PV=1.0 AC: DP 0:4987
FMuLV_amp_trim 214 . c . . FAILED DP=4991;AF=NaN;NP=0;PV=1.7976931348623157E308 AC: DP NA:NA
FMuLV_amp_trim 215 . t t . PASS DP=5007;AF=0.000;NP=1;PV=1.0 AC: DP 0:5007
FMuLV_amp_trim 216 . t t . PASS DP=5027;AF=0.000;NP=1;PV=1.0 AC: DP 0:5027
FMuLV_amp_trim 217 . a a . PASS DP=5013;AF=0.000;NP=1;PV=1.0 AC: DP 0:5013
(also have no Idea what is happening with the PV=1.7E308 I think it has something to do with indels)
Why SNVer doesnt detect the variants at 100% i do not know. All the variants are getting filtered out before the *raw.vcf is made.
I appologize if this is something dumb like a mapping or base qual scores. The reads are from an illumina MySeq if that helps. Quals are phred +33 (0-40).
Thanks in advance for any help or direction to resources,
Earl
SNVer is giving me a couple issues. Briefly, I set up a pileline utilizing Bowtie2, samtools sort/rmdup and SNVer for SNV calls. I have sample MySeq reads from Simian Immunodeficiancy Virus that map very well and call tons of low Pvalue variants with my pipeline. I have recently recieved new viral reads for a different project and no variants are called with the pipe. When I change from SNVer to samtools mpileup it calls 8 variants, which are all ~100% of the population. I have tried aligning with bwa as SNVer suggests with the same result.
*.raw.vcf file.
FMuLV_amp_trim 213 . c c . PASS DP=4987;AF=0.000;NP=1;PV=1.0 AC: DP 0:4987
FMuLV_amp_trim 214 . c . . FAILED DP=4991;AF=NaN;NP=0;PV=1.7976931348623157E308 AC: DP NA:NA
FMuLV_amp_trim 215 . t t . PASS DP=5007;AF=0.000;NP=1;PV=1.0 AC: DP 0:5007
FMuLV_amp_trim 216 . t t . PASS DP=5027;AF=0.000;NP=1;PV=1.0 AC: DP 0:5027
FMuLV_amp_trim 217 . a a . PASS DP=5013;AF=0.000;NP=1;PV=1.0 AC: DP 0:5013
(also have no Idea what is happening with the PV=1.7E308 I think it has something to do with indels)
Why SNVer doesnt detect the variants at 100% i do not know. All the variants are getting filtered out before the *raw.vcf is made.
I appologize if this is something dumb like a mapping or base qual scores. The reads are from an illumina MySeq if that helps. Quals are phred +33 (0-40).
Thanks in advance for any help or direction to resources,
Earl