pixy

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0 count of count_diffs and count_comparisons and all in count_missing

11

Hi, I used: bcftools mpileup -f reference.fa -b bamlist.txt -r chr10 | bcftools call -m -Oz -f GQ -o chr10-bcf.vcf.gz to get all sites vcf Then I used command: pixy...

hrluo93

**Describe the bug** A clear and concise description of what the bug is. **A reproducible example of the bug** Please include the following so we can debug the issue: (1)...

Jesuscs049

Hello, thank you for developing such a great software. I noticed two issues during my use of the manual: 1. GATK4 also generates multiple alleles, which can interfere with calculations...

zy66-su

Using pixy without an all sites VCF?

1

I have a fairly mundane need for pi and fst estimates that are in the ballpark but not necessarily the most accurate possible. We have a huge number of samples...

milesandersonmn

Hello, thanks for making such a useful tool! I am trying to run pixy to calculate pi on a masked vcf file that will often have one haplotype masked (i.e....

jamesfifer

Add support for arbitrary ploidy level (at least warn about incompatibility with polyploids)

1

Thank you for this tool! The idea is pretty elegant and we have been needing the "official" script to do these simple stats for so long... I understand that this...

taprs

ability to handle sex chromosomes

2

**Is your feature request related to a problem? Please describe.** The problem is that pixy seems unable to handle sex chromosomes. For example, the X chromosome is homogametic and thus...

jtweir

Hello, it's a great honor to communicate with you. In the process of using Pixy, it is very difficult for me to find the data in the sample script you...

tongtongy666

csi index

3

Hi! First, thank you for the nice program! I am currently working with lentil WGS data and the vcf cannot be tbi indexed but I found that Pixy does not...

giuliafrascarelli

Pixy can't handle simple VCFs (PLINK output)

2

Dear Kieran, Thank you for this wonderful tool! I have been using Pixy with standard, well-annotated VCFs, and everything goes correctly. Nevertheless, when I process my VCFs with PLINK, the...

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