Good morning Krishna,
I’m afraid I’m not a bcftools developer, so I have forwarded your problem to the samtools-help mailing list, in the hope that somebody there will be able to help you.
Jennifer
Begin forwarded message:
From: Krishna Prasad Acharya <kp...@ca...<mailto:kp...@ca...>>
Subject: Humble request and help_replacing variants that failed quality metrics with "N" with bcftools [EXT]
Date: 2 November 2022 at 04:33:13 GMT
To: "jen...@sa...<mailto:jen...@sa...>" <jen...@sa...<mailto:jen...@sa...>>
Dear Dr. Jennifer,
Good Morning!
I am Krishna Prasad Acharya, an MPhil student at Cambridge Vet School, Cambridge, UK. I am trying to use variant calling using the metrics of DP>=10, %QUAL>=30 and mapping MQ>30 and prepare a whole genome alignment. Everything was working well. However, I had an issue replacing "variants that did not pass filtering" with "N". Could you please help me fix this issue? I am requesting you because you are the developer of bcftools, so I thought you can help me to fix this issue. Attached is the file containing the code.
I hope you will help me fix this issue.
Thank you.
Regards,
Krishna Prasad Acharya
MPhil Student
Cambridge Vet School
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