xiucz
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Latest activity by xiucz-
xiucz commented,
Can you share the canonical gtf file? Thanks a lot!
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xiucz commented,
Genevieve Brandt (she/her) I have uploaded the files, and the name is /xiucz .
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xiucz commented,
Hi , Genevieve Brandt (she/her) 1. First, I set `-emit-lod ` to 0, the site still can't be called. 2. Using --genotype-germline-sites true, and my command line as below, the site still can't be ca...
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xiucz commented,
And a raw subset but not downsampling recalibrate.bam was here https://drive.google.com/drive/folders/1VaHbD2_SJokCbnXNAp-UId-4bNIWGtf-?usp=sharing Best, xiucz
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xiucz commented,
Hi , Genevieve Brandt (she/her). Following your advice, 1. Keeping the germline resource and interval padding parameters still give the result( force calling mode can call the site, while normal mo...
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xiucz commented,
Sorry , maybe GGA(genotype given alleles) is an old saying for `force-calling mode`. In this section (iv) Force-calling mode of https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mut...
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xiucz commented,
Hi, Genevieve Brandt (she/her) After reading this article and try the parameters, I still can't find the way to solve my problem. I think my dataset is not so particular, can you take a look at it...
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xiucz created a post,
GGA-mode gives PASS tag while the site failed in the normal workflow
GATK version: gatk-4.2.2.0; I have a site `chr3:178936091 PIK3CA c.1633G>A,p.E545K` that should be called in the usual workflow, but it failed. #normal workflow: ``` $gatk Mutect2 \-R ~/hg19/gatk...
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xiucz commented,
Shahryar Alavi Thank you . How about setting `--ploidy ` to `1` for HaplotypeCaller to run on microbial genomes? Best, xiucz
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xiucz commented,
hi, why not use `Haplotypecaller` to call variants in microbial genomes? Thank you .