smk_84
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Latest activity by smk_84-
smk_84 commented,
So my confusion is whether the two values are for ref and alt alleles or it is for the samples. e.g. [30, 30] [60, 60] is it ["Sample1 MMQ","Sample2 MMQ"] ? #in this case it is tumor-normal pair ...
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smk_84 created a post,
Minimum median mapping quality output query
REQUIRED for all errors and issues: a) GATK version used: 4.2.3.0b) Exact command used: ```FilterMutectCalls --output mutect.filtered.vcf.gz --variant mutect.vcf.gz --reference /storage1/fs1/bga/Ac...
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smk_84 created a post,
Hi Can you please point me to the chain file for human_g1k_v37_decoy to hg19 conversion
AnsweredHi, I need to liftover coordinates from human_g1k_v37_decoy to hg19. I can't seem to find the chain file for the same in the gatk resource bundle. Can you please point me to it if it is available s...