selscan --xpehh

I am trying to run selscan --xpehh by vcf file but I have missing genotype (./.) in vcf file, and I got this error ERROR: Alleles must be coded 0/1 only. How can I fix that error?

Also I have missing genotype for most of SNPs.

selscan

• 711 views • link

updated 2.5 years ago by Ram

• written 2.5 years ago by sevda •

It's "missing" genotype, not "missed". I've edited your post and made that fix (along with others to make it more readable)

• 0 views • link

written 2.5 years ago by Ram

0 answers

No answers yet.

More posts like this

Selscan: ERROR: Alleles must be coded 0/1 only.
written 4.6 years ago by taniamahmood38 •

I am trying to run nsl statistics using selscan tool on a vcf file (created using freebayes). But i am getting this error ERROR: Alleles …
ERROR: Variant physical position must be monotonically increasing
written 4.6 years ago by reza

I want to calculate XPEHH for each SNP position. When I run the following command selscan --xpehh --vcf B10_beagle.vcf --vcf-ref D6_beagle.vcf --map MAP.map --threads 8 …
haplotype phasing related issues
written 6.8 years ago by kas •

Dear members, How to code the alleles in a phased file to 0/1? `Selscan` is showing : ERROR: Alleles must be coded 0/1 only.
XPEHH output file blank in SELSCAN
written 7.5 years ago by azizul •

I make a SELSCAN input file as .vcf file and a .map file with two population for XPEHH calculation. Reference population files contain the exact …
The same loci for XP-EHH by Selscan
written 7.9 years ago by Victor •

Hello, I try to use selscan to compute the value of xpehh by selscan. But when I try to run it. I got the error …
How to generate the map file for selscan?
written 8.1 years ago by Victor •

Hello I have 2 datasets and want to analysis the XPEHH scores by selscan. I used plink and beagle to pre-process my datasets. When I …
the XP-EHH instruction
written 8.1 years ago by Victor •

Hello, I am trying to get the XP-EHH values by using HP-EXX. (https://github.com/joepickrell/xpehh) . I only have map and ped plink files in two populations. …
vcftools keep only indels not working
written 8.7 years ago by t86dan •

Hi, I am trying to filter a vcf file so that I only get indels from it. I am using vcftools with the following command: …
Forcing A1/A2 alleles in PLINK in a VCF phased file
written 8.9 years ago by GabrielMontenegro

I have a phased VCF file and I need to change the alleles of the SNPs so that the alleles coded as 0 represent the …
Is there a way to phase an unphased data for selection detection?
written 11.9 years ago by eyb

<p>Hi!</p> <p>I have ped/map file containing two populations (~110 samples, ~500k SNPs). Is there a software which can phase the data? Alleles should be coded …