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tfwillems / HipSTR

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
GNU General Public License v2.0
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filter_haploid_vcf.py #72

Closed JiruHan closed 4 years ago

JiruHan commented 4 years ago

Hello, I'd like to inquiry the problems that I meet, when I run filter_haploid_vcf.py, I have some error below: Traceback (most recent call last): File "scripts/filter_haploid_vcf.py", line 281, in main() File "scripts/filter_haploid_vcf.py", line 137, in main gt_a = int(sample['GT']) ValueError: invalid literal for int() with base 10: '0|2' Could you please take a look? Thanks in advance!

tfwillems commented 4 years ago

Hi @JiruHan,

Hopefully you managed to resolve your issue, but it's caused by the fact that your VCF contains diploid genotypes, not haploid genotypes.

If you're genotyping a haploid chromosome, make sure you specify --haploid-chrs while running HipSTR and you can then use this script.

If you're genotyping a diploid chromosome, you'll want to use the filter_vcf.py script instead.

JiruHan commented 4 years ago

Hi there,

Many thanks for your reply! I have solved the problem, before I use --hap-chr-file, now I add --haploid-chrs, and it’s working. Thanks so much for your time!

Best wishes, Jiru

From: tfwillems notifications@github.com Reply-To: tfwillems/HipSTR reply@reply.github.com Date: Wednesday, March 11, 2020 at 1:15 AM To: tfwillems/HipSTR HipSTR@noreply.github.com Cc: Jiru Han han.ji@wehi.edu.au, Mention mention@noreply.github.com Subject: Re: [tfwillems/HipSTR] filter_haploid_vcf.py (#72)

Hi @JiruHanhttps://github.com/JiruHan,

Hopefully you managed to resolve your issue, but it's caused by the fact that your VCF contains diploid genotypes, not haploid genotypes.

If you're genotyping a haploid chromosome, make sure you specify --haploid-chrs while running HipSTR and you can then use this script.

If you're genotyping a diploid chromosome, you'll want to use the filter_vcf.pyhttps://github.com/tfwillems/HipSTR/blob/master/scripts/filter_vcf.py script instead.

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