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contig info for header is extracted from bam #38

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merged 2 commits into from
May 8, 2024
Merged

contig info for header is extracted from bam #38

merged 2 commits into from
May 8, 2024

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kubranarci
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contig info is extracted from tumor bam files instead of fasta.
samtools view -H is used to get contig info which is then converted into vcf header format using awk.

@kubranarci kubranarci self-assigned this Apr 30, 2024
@kubranarci kubranarci linked an issue Apr 30, 2024 that may be closed by this pull request
generete contig from bam not fai #36
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@kubranarci kubranarci requested a review from NagaComBio April 30, 2024 08:22
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NagaComBio approved these changes May 8, 2024
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The standard VCF headers are from the BAM file now as expected for this PR. So, we can merge it.

@kubranarci kubranarci merged commit b60a339 into main May 8, 2024
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@kubranarci kubranarci deleted the 36-generete-contig-from-bam-not-fai branch May 8, 2024 12:49
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generete contig from bam not fai
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