Yanis Chrys
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Activity overview
Latest activity by Yanis Chrys-
Yanis Chrys commented,
Hi Genevieve Brandt (she/her) Thank you for getting back to me. As it turns out my workaround was to use --remove-unused-alternates and then filter for the AD.1 of the SNP (because then only SNPs w...
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Yanis Chrys commented,
Yes, for now excluding filtered variants and using a complex JEXL string to catch anything that isn't trusworthy seem like the best option.Thank you for looking into that problem because it appears...
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Yanis Chrys commented,
Hi Pamela, Thank you for your reply. It does work, yes. Although, I now think that it would be best to just snpmask MNPs and MIXED sites completely because the tool says it doesn't deal with them ...
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Yanis Chrys created a post,
How do I tell FastaAlternateReferenceMaker to only replace properly called sites?
AnsweredHi,I am trying to create a consensus fasta sequence from vcf files made with GVCF HaplotypeCaller and I want to make sure only sites that fulfill certain requirements are replaced and everything el...
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Yanis Chrys commented,
Additionally, I was wondering if you can tell me if FastaAlternateReferenceMaker can correctly choose the right alternate allele.In the above example, if the 3rd one is called in one sample and the...
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Yanis Chrys created a post,
JEXL expression for filtering on AD (SelectVariants / FastaAlternateReferenceMaker)
Hi,I am working on haploid bacterial data and I ran into a limitation of the program that I either can't solve or it would be nice to add a funtion for it in the future. I'll explain the issue: Let...