Update for pool seq

[seynard]

You mention in the READme that a future plan was to develop a tool to extract fragment sequences from bam files of pool. Did you implement this option? Or is it available in HapCut2 (I didn't find anything about pool seq data in there).
Thanks in advance for your help. Best regards.

[vibansal]

The extractHAIRS module in the HapCUT2 repository should be able to extract fragment sequences from bam files of pooled data. Note that you will have to specifiy a VCF file with diploid genotypes as input (0/1 for hets).

[seynard]

Thanks a lot for your answer and the tip. I'll definitely try it out. But then if I only have pool data information I need to create a vcf with 'average' genotype then? Thanks again for the help.

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On Fri, 19 Jan 2024, 22:58 Bansal Lab, ***@***.***> wrote: The extractHAIRS module in the HapCUT2 repository should be able to extract fragment sequences from bam files of pooled data. Note that you will have to specifiy a VCF file with diploid genotypes as input (0/1 for hets). — Reply to this email directly, view it on GitHub <#9 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AH7AX7LWT4U2IQQH37TRD6TYPLUBXAVCNFSM6AAAAABCAFZLNKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBRGE3TKMBUG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[vibansal]

The genotype is only used to identify heterozygous sites. So, all genotypes with at least one copy of the two alleles can be represented as 0/1.

[seynard]

Ok perfect. I'll try that. Thanks again for your help

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On Fri, 19 Jan 2024, 23:37 Bansal Lab, ***@***.***> wrote: The genotype is only used to identify heterozygous sites. So, all genotypes with at least one copy of the two alleles can be represented as 0/1. — Reply to this email directly, view it on GitHub <#9 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AH7AX7M3ZKZ3EFILOGEPIKTYPLYTRAVCNFSM6AAAAABCAFZLNKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBRGI2DANZWGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>