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
1 answer
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
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Thank you so much!! I'm going to perform bedtools complement
Best wishes,
Yocelyn
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