bedtools and SNPs for pyseer-GWAS analysis

Question

[3335098459]

Hi

I have used snippy package for SNP calling and later on used those for pyseer-GWAS analyses. But it seems that this command of bedtools cannot read the vcf files.

bcftools merge -m none -0 -O z *.vcf.gz > merged.vcf.gz

I am getting this error:

bcftools: Relink /root/miniconda3/bin/../lib/./libgfortran.so.4' with /lib/x86_64-linux-gnu/librt.so.1' for IFUNC symbol `clock_gettime'

Failed to open 100010367.vcf.gz: could not load index

Is there anyone having this kind of experience with pyseer before? Is there any problem with bedtools or vcf files?

Regards

Awan

Answer 1

[ATpoint]

Failed to open 100010367.vcf.gz: could not load index

Is the file indexed? Did you try to re-index?

[3335098459]

After your reply, I have used other packages to generate indexed vcf file.

vcfcombine *.vcf > merged.vcf (I guess there was some issue with bedtools)

bgzip -c merged.vcf > snps.vcf.gz

tabix -p vcf snps.vcf.gz

Thanks for pointing out the direction.

[ATpoint]

Glad it worked. Our of interest, what did you use to index before? The reason you need bgzip over standard gzip is that bgzip does blockwise compression so tools can random-access the file by only decompressing the relevant part of that file.

[3335098459]

Actually there was some issue with the bedtools/bcftools compiling code and installation. Previous wrapper tool also used bedtools for indexing and compression. While re-indexing I figured out this point and I used different tool to combine, compress and indexing. Also thanks for explaining the bgzip core concept.