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...@cam.ac.uk<mailto:kp...@cam.ac.uk>> 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: "jennifer.lid...@sanger.ac.uk<mailto:jennifer.lid...@sanger.ac.uk>" <jennifer.lid...@sanger.ac.uk<mailto:jennifer.lid...@sanger.ac.uk>> 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 Google Scholar: https://scholar.google.com/citations?user=N7lg6bAAAAAJ&hl=en [scholar.google.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__scholar.google.com_citations-3Fuser-3DN7lg6bAAAAAJ-26hl-3Den&d=DwMFAw&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=KoMRxlOPpFl6Xyyr0RoXf3uy3H2lQZNZP8OyP67Mr_4&m=3SiG0Zle08hFl3VmM7TerK5PaHKntciWlWeZlj5SpJYPpXxaUbMNa5vnHpVWVbnX&s=9bSdTvDBps8yxIPQyBfmsWUMvsMFeg_BUmhQX0gsrjY&e=> Researchgate: https://www.researchgate.net/profile/Krishna-Prasad-Acharya-2 [researchgate.net]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Krishna-2DPrasad-2DAcharya-2D2&d=DwMFAw&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=KoMRxlOPpFl6Xyyr0RoXf3uy3H2lQZNZP8OyP67Mr_4&m=3SiG0Zle08hFl3VmM7TerK5PaHKntciWlWeZlj5SpJYPpXxaUbMNa5vnHpVWVbnX&s=EZvrKzjn09xsHppj_UhftYTnFm4ROC4r-_2kqg-uOvE&e=> Scopus https://www.scopus.com/authid/detail.uri?authorId=57226349259 [scopus.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.scopus.com_authid_detail.uri-3FauthorId-3D57226349259&d=DwMFAw&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=KoMRxlOPpFl6Xyyr0RoXf3uy3H2lQZNZP8OyP67Mr_4&m=3SiG0Zle08hFl3VmM7TerK5PaHKntciWlWeZlj5SpJYPpXxaUbMNa5vnHpVWVbnX&s=GXpodFwdiY4rLWbHLsHW6K2YpFbLOWk32TybD106t4M&e=> ORCID: https://orcid.org/0000-0002-4208-7592 [orcid.org]<https://urldefense.proofpoint.com/v2/url?u=https-3A__orcid.org_0000-2D0002-2D4208-2D7592&d=DwMFAw&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=KoMRxlOPpFl6Xyyr0RoXf3uy3H2lQZNZP8OyP67Mr_4&m=3SiG0Zle08hFl3VmM7TerK5PaHKntciWlWeZlj5SpJYPpXxaUbMNa5vnHpVWVbnX&s=m0jeaYXSPt9j7u6RTOhfl3TS1y8Vx1P62If4OG34XJI&e=> Publons: https://publons.com/researcher/3703799/krishna-prasad-acharya/publications/ [publons.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__publons.com_researcher_3703799_krishna-2Dprasad-2Dacharya_publications_&d=DwMFAw&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=KoMRxlOPpFl6Xyyr0RoXf3uy3H2lQZNZP8OyP67Mr_4&m=3SiG0Zle08hFl3VmM7TerK5PaHKntciWlWeZlj5SpJYPpXxaUbMNa5vnHpVWVbnX&s=UmLDrWTCkujcZ-o2jT3PkZUxWGQoa9jsh2LYVGgSeCo&e=> "Imagination is more powerful than knowledge" Albert Einstein -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
Script_replace quality metrics failed bases with N.docx
Description: Script_replace quality metrics failed bases with N.docx
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