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I have in interesting case where the stutter model fails to converge. My goal is to force STR to genotype these sites, as I have a few false-negatives that have great coverage.
After increasing th…
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These fields need a description:
- sptype?
- inttype?
- IS6110?
- RFLPfamily?
- spfamily_parentstrain?
- PGG?
- spoligo_octal?
Also can you explain what h34rv i…
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Hi
What would be the best way to output active regions from GATK4 HaplotypeCaller?
In GATK 3.x, an option `--activeRegionOut ` could be used to write active regions in a TSV file. However, I am …
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Hello,
Trying to compile vt using gcc 4.4.7 on CentOS 6 and having issues with svm_train.cpp
[root@HPC05 ~]# uname -a
Linux HPC05 2.6.32-573.12.1.el6.x86_64 #1 SMP Tue Dec 15 21:19:08 UTC 2015 …
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Any plan on this? Thanks
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When I do `bcftools view -i 'MQRankSum="."'`, then this record is printed:
10 67402 . C A 52.98 . ABHom=1;AC=2;AF=1;AN=2;BaseCounts=2,0,0,0;DP=2;Dels=0;ExcessHet=3.0103;FS=0;GC=41.65;HaplotypeS…
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Hi,
I'm running SV2 (v 1.2) on some human WGS samples, but I keep getting this error (copied below).
The txt file is generated, but no vcf. I tried different callsets in vcf and bed formats, and…
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It's time to talk about variant calling (again). While working on a bit of a [side project](https://github.com/edawson/hpv_minION_analysis) we started imaging certain things we needed for really great…
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Core Hunter 1 and 2 only supported multi-allelic marker data in frequency format. The frequency table was given as marker-allele x individuals which is unconventional. For Core Hunter 3 we will follow…
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```
From Ben on 3/5/13:
I am trying to find Bis-SNP results for single-lane TCGA samples. For
the following lanes, I can find TDF files but not 6plus2.bed files.
Can either of you see why? Zack co…