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Issue with prepare_files vcf file sorting #9

Open krovi137 opened 1 month ago

krovi137 commented 1 month ago

Hello,

I am attempting to use MMARGE for analyzing ATAC-seq data from different strains of mice. I downloaded the SNP and Indel vcf files from the Mouse Genomes Project website and sorted them using bcftools sort. However, I keep receiving an error when I use prepare_files that says the vcf file is not sorted:

grep: write error: Broken pipe File Sorted_SNPs.vcf is not sorted! Please sort file! grep "^#" Sorted_SNPs.vcf > sorted file grep -v "^#" Sorted_SNPs.vcf | sort -k1,1 -k2,2n >> sorted file

I also sorted the file as described using the grep command but that does not seem to get rid of the error. I've also attempted to run the prepare_files command with the -no-check flag but even with that, it checks to see if the vcf files are sorted. Please help!!

Thanks so much! Harsha

vlink commented 1 month ago

Hi,

Can you send me the link to the files you downloaded, so I can debug it?

Thanks!

krovi137 commented 1 month ago

Hi! Thanks so much for your response!

Here's the link I used: https://www.mousegenomes.org/snps-indels/

I downloaded the SNPs/Indels for mm39. Please let me know if you need anything else from me.

Thanks again!

krovi137 commented 2 weeks ago

Hello,

I was wondering if you had had a chance to look into the bug perhaps? Please let me know.

Thanks so much!