Question: extractPIRs is throwing an ERROR
0
gravatar for nkausthu
2.4 years ago by
nkausthu30
nkausthu30 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 • 554 views
ADD COMMENTlink modified 2.4 years ago by genomax89k • written 2.4 years ago by nkausthu30

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

ADD REPLYlink written 2.4 years ago by genomax89k

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 2.4 years ago by nkausthu30

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 19 months ago by schmidemanuel40
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