
yqiu
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Activity overview
Latest activity by yqiu-
yqiu commented,
Thanks for the quick response and suggestions! I tried them separately. Unfortunately, neither parameter can rescue the variants. I tried --initial-tumor-lod 1 and --active-probability-threshold d...
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yqiu commented,
Hi Genevieve, Thanks for the response and the link you shared is very useful. But it may not directly relate to my question. I get that there are some reads are uninformative and they are not count...
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yqiu commented,
Hi Genevieve, Thanks for the response! Please see the answers to your questions below. Here is the SNV as called in GATK 4.1.8.1. CHROM POS . C T . . AS_SB_TABLE=9605,9821|113...
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yqiu commented,
Hi Genevieve, Thanks for the detailed response! Do you have any suggestions about which parameter to adjust and suggested values? Or should I adjust both of them? For --initial-tumor-lod, should I ...
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yqiu commented,
Thanks a lot for the suggestion! Following your previous advise, we did use --max-reads-per-alignment-start to 0 in both GATK 4.1.8 and GATK 4.2 in the results I mentioned above.
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yqiu created a post,
Target variants not in active region
AnsweredWe have a known SNV with AF ~1% and are trying to use Mutect2 to detect it in amplicon sequencing data. It can be called with no problem in some samples but cannot be called in other samples. The...
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yqiu created a post,
Mutect2 AF does not match AD and DP
AnsweredWe have one indel detected by Mutect2 but the AF reported does not match AD and DP. As shown below, AF is 0.425 and 0.134 for two alternative alleles. But AD is only 258 and 255 respectively with 1...
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yqiu created a post,
Variants missing in 4.2.0.0 due to assembly cycles
AnsweredWe have a known SNV with AF ~1% and are trying to use Mutect2 to detect it in amplicon sequencing data. It can be called with GATK 4.1.8.1 without problems in multiple samples. It cannot be calle...
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yqiu commented,
Hi Genevieve, Sorry for the delay in response. Thanks for the suggestion. We have no problems when disable subsampling as you suggested. Best, Yunjiang
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yqiu commented,
Hi Genevieve, Thanks a lot for the prompt reply. Could you help explain a little bit more about why "Not necessarily 4000 would be a subset of 12000"? There might be something about downsampling t...