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generete contig from bam not fai #36

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kubranarci opened this issue Apr 29, 2024 · 0 comments · Fixed by #38
Closed
2 tasks done

generete contig from bam not fai #36

kubranarci opened this issue Apr 29, 2024 · 0 comments · Fixed by #38
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kubranarci commented Apr 29, 2024 •
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Have you checked the docs?

Description of the bug

platypus does not add #contig info to vcf header, which is againist standard vcf format which we report in the last step of the pipeline.

#contig lines are made to add from fai, which whould be from input BAM.

#contig lines should be generated from BAM files not from fai.

commend done by @NagaComBio

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@kubranarci kubranarci added the bug Something isn't working label Apr 29, 2024
@kubranarci kubranarci self-assigned this Apr 30, 2024
@kubranarci kubranarci linked a pull request Apr 30, 2024 that will close this issue
contig info for header is extracted from bam #38
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contig info for header is extracted from bam ghga-de/nf-platypusindelcalling
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