Charity Goeckeritz
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Activity overview
Latest activity by Charity Goeckeritz-
Charity Goeckeritz commented,
Hi Gökalp, Thanks so much for your response! I was checking the files this morning and found that some of them are getting further - I saw one had reached up to chromosome 8. As far as I can tell i...
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Charity Goeckeritz created a post,
HaplotypeCaller traversing all chromosomes, but they aren't in the output gvcf...
Hi there, I am using HaplotypeCaller in GATK v 4.0.11.0. I am giving each run 34Gb of memory and 12 threads, but each run hardly makes it through chromosome 2 (there are 17 total chromosomes) give...
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Charity Goeckeritz created a post,
How do I know if the PED file is actually being used...?
Hi there, I have a few questions surrounding how the pedigree information works... I have 13 samples: mom, dad, and 11 progeny. The organism is a plant where sex is irrelevant. 1. (How does / Doe...
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Charity Goeckeritz created a post,
Equivalent tool for MergeBamAlignment's Primary_Alignment_Strategy=Most Distant?
Hi there, I have an allopolyploid genome that is mostly phased. I've mapped 150bp PE reads to this genome, and there's of course -- a ton of multimappings. I used BWA-MEM for this with the -M flag...