Questions tagged [wes]
The wes tag has no usage guidance.
13
questions
0
votes
1
answer
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A bash script for running on a bunch of bam files
I have some bam files in this directory
/data/Continuum/WES/results/
I want to run GATK mutation calling over bam files
I ...
- 1,981
3
votes
0
answers
50
views
Issue creating CNV plot from WES data
I received Whole Exome Sequencing data from an NGS company (CARIS, specifically). I received R1 and R2 FASTQ files, a BAM file aligned to hg38, and a VCF file.
I used CNVPytor to create a CNV plot (...
1
vote
1
answer
51
views
Importing local files to a GATK docker image
I have pulled GATK docker on my computer but when running a GATK command, can not locate my input file
My OS version
...
- 1,981
1
vote
0
answers
25
views
Which type of variant caller should I use in a WES normal cell line sample?
I have whole-exome sequencing data of an immortalised non-tumor (normal) cell line that I wish to assess for the presence/absence of APC/Wnt mutations. This is to double check that the cell line is ...
- 181
3
votes
0
answers
85
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Picard's CollectGcBiasMetrics gc-bias plot- help with interpretation
Setup
I ran picard's CollectGcBiasMetrics tool for my WES sample, with the intention of assessing the performance of the Exome capture panel in terms of the uniformity of read coverage at various %GC ...
- 181
2
votes
0
answers
23
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Off-target % for whole-exome sequencing panel
My samples have been sequenced with the Twist Exome 2.0 sequencing panel, and I want to assess how efficient the sequencing has been. By efficient, I mean examining metrics such as the uniformity (...
- 181
2
votes
1
answer
56
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WES variant calling with DNBSEQ-T7: technical quality assessment
I recently received whole exome sequencing samples that were sequenced on an MGI sequencing instrument, DNBSEQ-T7. I am interested in somatic variant-calling on the paired tumor-normal samples. As ...
- 181
2
votes
1
answer
101
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Is it common to get different number of SNVs+Indels across samples from vcf files generated using GATK and DRAGEN (counts are higher for GATK)?
We have 2 vcf (Whole Exome Sequencing (WES) data; germline samples) files (e.g., vcf_1 and vcf_2). vcf_1 was generated (Ref. genome: hg38) using the GATK pipeline for 250 children and their parents ...
- 21
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votes
1
answer
1k
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What are values of FILTER column of vcf files produced by Mutect2
I have called SNVs with Mutect2, now in filter column of a file called filtered vcf I have a lot of things like
...
- 1,981
-1
votes
2
answers
255
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Error in running Mutect2
I am trying to run Mutect2 on a .bam file but I get an error by Googling can not be tackled
Have you seen this error?
...
- 1,981
-4
votes
1
answer
234
views
Getting error in running GATK
I am trying to making a fasta doc using GATK tools but I don't know what does this error say
Server2:/data2/RNASeq/Angel/gatk$ ./gatk CreateSequenceDictionary -R reference.fa
Using GATK jar /data2/...
- 1,981
-3
votes
1
answer
581
views
Extracting a column from a vcf file
I have a zipped vcf file of dbSNP hg38 version
No space left on my device to unzip that
I want to extract a column from that
I have tried this
...
- 1,981
0
votes
0
answers
83
views
An error with annovar
I want to install annovar but in one particular part I always get this error
...
- 1,981