Hi everybody,
I am new analyzing WES and I try GATK4 workflow for the detection of somatic variants.
I run Mutect2 in tumor-only...
12 results in 0.0021 seconds.
-
GATK4 (4.1.2.0) Mutect2 --germline-resource option
-
dbSNP database for just NA12878
So I may be completely wrong here but please correct me since I'm mostly used to doing RNA splicing analysis.
I have sequenced sheared... -
heterozygosity and allele balance in NGS doubt
Hi,
I have data from a target enrichment on a few human genes, of course sequenced through NGS. Enrichment, sequencing and data analysis... -
Germline Mutations
hi everybody,
i was wondering, if i want to call germline mutations what allele frequency threshold should i choose to filter most of false... -
Allele frequency in sample below 10%
Hello,
In our pipeline we have a quality control step where 23 snps are called with GATK and with realtime PCR. Lately as the coverage... -
Calculating allele frequency from VCF file
Hi Members,
Please pardon me, if this have been asked previously.
I find no proper answered thread for this.
I have VCF... -
Annotate allele frequencies in a vcf file
Hi everyone,
I want to make you a question although maybe it is really simple and easy:
I'm working with exome sequencing. How...Last edited by Elurbe; 04-03-2013, 11:07 AM. -
Patchwork - allele-specific somatic CNAs in cancer (WGS)
We have developed an R package for allele-specific copy number analysis of whole genome sequenced tumor tissue, capable of handling normal cell content... -
region of significant allele sharing
Hi,
I would like to know if anyone knows of any tool that retrieves from a multi-sample .vcf file a query such as: all the genomic regions... -
An example, multi-sample VCF file?
Hiya folks,
Does anyone have a multi-sample VCF file (or at least a portion of one) that they'd be willing to share with me? I'm trying... -
Pysam pileup working unpredictably
Hi,
I'm trying to count allelic frequencies at SNPs and Pysam seems to be the best solution to do that. However, when I make a call to... -
Software for variant frequency
Hello all,
I used to be able to use CLC for my SNP calling, which generates the reference base and the frequency of the variant allele...
