search

stschiff / sequenceTools

Other
39 stars 10 forks source link

Does pileupCaller output reference bases? #5

Closed Arkkienkeli closed 5 years ago

Arkkienkeli commented 5 years ago

Hello, does it output all alleles like GATK3 GenotypeGVCF --includeAllSites ?

Arkkienkeli commented 5 years ago

@stschiff Could you please assist me on this? Thank you!

stschiff commented 5 years ago

Yes, it does if you don't give it a SNP list file.

Arkkienkeli commented 5 years ago

@stschiff Hi Stephan, thank you for the response. Still, I get all 0 in geno file (EigenStrat output). From eigenstrat site: 0 means zero copies of reference allele. I don't get any 1 or 2 in geno file.

pileupCaller --sampleNames fileq20Q20 --minDepth 1 -o EigenStrat -e filecall20Q20 < s-fileq20Q20.txt

I tried --minDepth 2 also, and I also tried decreasing to q10\Q10 in samtools mpileup. In this case, it produces more SNPs in output, but still all 0 in geno file.

stschiff commented 5 years ago

Not quite sure I follow this. Have you checked the pileup-output itself, before piping into pileupCaller? Have you checked that your samtools command works as expected, outputting all sites, with the correct reference and alternative alleles, and the expected pileup information?

On 3. May 2019, at 17:26, Nick notifications@github.com wrote:

@stschiff https://github.com/stschiff Hi Stephan, thank you for the response. Still, I get all 0 in geno file (EigenStrat output). From eigenstrat site: 0 means zero copies of reference allele. I don't get any 1 or 2 in geno file.

pileupCaller --sampleNames fileq20Q20 --minDepth 1 -o EigenStrat -e filecall20Q20 < s-fileq20Q20.txt

I tried --minDepth 2 also, and I also tried decreasing to q10\Q10 in samtools mpileup. In this case, it produces more SNPs in output, but still all 0 in geno file.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stschiff/sequenceTools/issues/5#issuecomment-489134733, or mute the thread https://github.com/notifications/unsubscribe-auth/AADNBGTXZ3C4XPUBUAI4EX3PTRKQXANCNFSM4HGWOLJA.