Question: extractPIRs is throwing an ERROR
gravatar for nkausthu
24 months ago by
nkausthu20 wrote:

I am getting an error while using extractPIRs as follows

./extractPIRs --bam bamlist --vcf VCF.gz --out

Reading genotypes in [/MOD_recalibrated_variants.vcf.gz] in VCF format
  * 477 samples
ERROR: Duplicate site pos=52264013 ref=C alt=T

How can I avoid this kind of scenario? Thank you

phasing extractpirs shapeit • 470 views
ADD COMMENTlink modified 24 months ago by genomax80k • written 24 months ago by nkausthu20

Looks like the program is telling you what the error is.

ADD REPLYlink written 24 months ago by genomax80k

Yes .. Programs tells that its duplicate site position but its in different chromosome. But I think it wont be correct if I delete one.

ADD REPLYlink written 24 months ago by nkausthu20

This is rather for further references as this one is really old. If you check their documentation on manual the state:

NOTE : the VCF file should contain SNPs from only one chromosome.

So, it cant handle different chromosomes the same time and you need to split them prior continuing.

ADD REPLYlink written 14 months ago by schmidemanuel40
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