I am currently trying to run bcftools call on a large bcf file and I keep receiving the "Segmentation fault" message. I use the latest version of bcftools (1.3.1). I am using: bcftools call -v -c -f gq in.bcf > out.bcf
I successfully used bcftools call in the past on various files and never had this problem before. The only difference here is that I slightly changed my workflow and now filter for depth directly on my bcf file, not on my vcf. Here is my workflow
- samtools mpileup on a set of bam files
- vcftools --bcf file.bcf --min-meanDP 5 --max-meanDP 25 --recode-bcf --out file_depth_filtered
- bcftools call -v -c -f gq file_depth_filtered.bcf > out.bcf
In the past, I use to make a vcf file from my bcf right after step 1 and filtered directly on my vcf file. This worked just fine. Also, using bcftools call on my none-filtered bcf file works well. So basically, there is something wrong in my filtered file.
The error I receive from my HPC is "line 11: 3165 Segmentation fault (core dumped) bcftools call -v -c -f gq file_depth_filtered,bcf > out.bcf
What do you think could be causing this?