xiucz
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Latest activity by xiucz-
xiucz commented,
SkyWarrior Thanks for your solution！
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xiucz commented,
Another example, ``` chr10 123241348 . A *,T,<NON_REF> 7814.01 . DP=737;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQandDP=2626991,737 GT:AD:DP:GQ:PL:SB 1/2:...
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xiucz created a post,
How to avoid "*" in HaplotypeCaller or GenotypeGVCFs step ?
Hi, I cannot find any arguments to avoid the * in the vcf results. GATK version: 4.2.3.0 ``` #HaplotypeCaller chr9 136599534 . TTCATTCATTCATTCAC T,*,CTCATTCATTCATTCAC,<NON_REF> 391...
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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 call...
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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 mode...
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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? ...