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Hi (again).
I'm getting a parsing error for the following variant.
```
chr2 66534523 . G C 38.3 .AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.5…
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Hi I'm running xcltlk baf with the provided vcf but it looks to be failing to parse?
```
(venv) chang@nidus:/media/sdl/chang/jd/GW14_TS$ xcltk baf --label GW14_TS --sam trimmed_Aligned.sortedByCoord…
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Hi,
I am trying to give vcf file as input for SV generated from Svaba, Manta and Gridds but getting an error 'VCF appears to contain multiple samples or non-standard fields. Please provide a single-s…
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Hi,
I'm just wanting to check in regarding how to obtain an all-sites VCF using snpArcher. From what I can tell, I just need to add the -all-sites flag to the GenotypeGVCFs command in the following…
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Hi,
I am trying to use vcfView for the first time and I have pulled the latest committ as well as the last release, but the "Select VCF" button is not working; could you please advise?:
![image](htt…
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Hi author,
I just use this tool to call SV for trial on GIAB's benchmarking set. However, the vcf output is different from standard form in which the REF and ALT is replaced with N and SV/CSV. Alth…
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Hi Jody,
The VCF produced by TbProfiler v6.3 violates the VCF v4.2 specification which might cause issues with parser and genome browsers. TbProfiler reports GQ values as Floats but the specificati…
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@sandve, I am working on reconstructing a haploid haplotype using the imputed genotypes from KAGE. Currently, I am using the following commands:
```bash
kage index -r MHC-CHM13.ref.fa -v MHC_49-M…
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Hi,
I ran with the following command line for RDD:
java -jar $scriptPATH/JACUSA_v2.0.4.jar call-2 -p $nCPUs -F 1024 -a I,B,S,M,H:condition=1 -r $outPATH/$outFILE -f V -b $bedPATH/$bedFILE -R $genP…
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Hey there,
I'm trying to run your tool but I think it expects the vcf files to have a specific FORMAT column.
`grep --color=auto -v '^#' $WT | \
awk '{split($10,a,":");if(a[4]>=int("'$COV'") …