Feedback on SNP filtering step before running PSMC

fcr

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Join Date: Jan 2012

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Feedback on SNP filtering step before running PSMC

02-12-2013, 03:41 AM

Dear All,

I would like to apply a stringent filter before obtaining the diploid.fq.gz needed as input for PSMC.
I was reading the Li & Durbin 2011 paper "Inference of human population history from individual whole-genome sequences" there is actually an extra filtering step for SNPs, probably using samtools.pl varFilter.

I do have 26X samples. Do you think this slight modification of the pipe makes sense?

samtools mpileup -C50 -uf ref.fa aln.bam| samtools.pl varFilter –Q25 –q10 –d3–D120 –G25 –w10 –N2 –l30 - | bcftools view -c - | vcfutils.pl vcf2fq –d3 -D 100 |gzip > diploid.fq.gz

I would appreciate any feedback
Cheers,
Nando
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