vcfAllSiteParser does not work

Question

[YocelynGG]

Hello!!

I have been trying to perform the MSMC pipeline. I have 6 vcf files (obtained with GATK). I want to obtained the masked bed files and their corresponding vcf files. I have been performing the script: vcfAllSiteParser.py but it doesn't work. The output is empty (file.bed and file.vcf), even after running for a long time. I'm running the commands:

vcfAllSiteParser.py file1_GATK.vcf file1.bed > file1_new.vcf

And, I have changed the name of the script:

vcfCaller.py file1_GATK.vcf file1.bed > file1_new.vcf

Someone could help me to figure out a solution?

Thank you so much !!

Best wishes,

Yocelyn

[Pierre Lindenbaum]

cross-asked: https://github.com/stschiff/msmc-tools/issues/11

[YocelynGG]

Thank you so much!! I'm going to perform bedtools complement

Best wishes,

Yocelyn

[Pierre Lindenbaum]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Answer 1

[Pierre Lindenbaum]

want to obtained the masked bed files and their corresponding vcf files.

may be you just want to use bedtools complement to get the complement of the bed and then bcftools view with option --regions-file