Questions tagged [wes]
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16 questions
1 vote
0 answers
49 views
Hard Filtering Differences between WES and WGS
I am working on human WGS data and i need to detect SNPs and INDELs, during the variant calling step i have to use a filter to remove false SNPs or in general bad quality SNPs, i am wondering if I ...
2 votes
0 answers
72 views
Variant missing in WES Analysis
I hope you are all doing well. I analyzed the FASTQ files (WES) from a patient with symptoms of deafness on a rented server. I identified the specific variant and reported it. I no longer want to use ...
4 votes
0 answers
142 views
PLINK to VCF seems to to not convert correctly, what am I missing
I have Illumina Infinium Global SNP array data that I want to compare to same sample WES data in VCF format. To do that, I am trying to convert the plink files (.bed, .bim and .fam) into vcf. I am ...
- 453
0 votes
1 answer
233 views
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 ...
- 2,242
3 votes
0 answers
148 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 (...
2 votes
1 answer
99 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 ...
- 2,242
1 vote
0 answers
42 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
271 views
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
54 views
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
93 views
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
4 votes
1 answer
197 views
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 ...
- 41
0 votes
1 answer
2k views
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 ...
- 2,242
0 votes
2 answers
336 views
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? ...
- 2,242
-4 votes
1 answer
283 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/...
- 2,242
-3 votes
1 answer
689 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 ...
- 2,242