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I tried to run the snpfilter.sh to obtain the vcf file for uncovering the allele-specific copy number alternations in the tumor samples. I prepared tumor bam file, common dbSNP vcf file, and hg38.fa, …
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There seems to be confusion surrounding the use of the GT and AD keys in the INFO field.
The GATK Mutect2 tool would produce a VCF file containing the following GT:AD values for a sample containing…
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For example,
| | Chromosome | Start_Position | End_Position | Reference_Allele | Tumor_Seq_Allele1 | Tumor_Seq_Allele2 | NCBI_Build |
---|---|---|---|---|---|---|---
**input**| 11 | 108151707 | 1…
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Hello,
Did you apply the survival prediction on slide level or patient level? If it is on patient level can you please let me know how did you convert the slide level prediction to patient level pr…
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There is a bug that occurs only when the normal/control sample name contains "-." This bug makes this script look for a non-existent vcfMergerAC (alleleCount version) pass file. The problem occurs in …
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### Need
The number of SVs uploaded to Scout for WGS cases in balsamic is much higher than is common, and could really benefit from being reduced. As an example here are the some values from the mo…
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Hi
I have tumor-only WGS, consisting of nodulous and tumorous tissue.
Your program is very interesting because filtering germline mutations in these samples have seemed very difficult and almost imp…
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I tried running lofreq with the `call` option:
```
lofreq call -s -S /path/to/dbsnp_147_b37_common_all_20160601.vcf -f \
/path/to/Homo_sapiens_assembly19.fasta -o /path/to/output.vcf /path/to/tu…
vymao updated
4 years ago
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Hi,
Thank you for developing this tool which is quite easy to use!
I am wondering if SpecHLA could also be used to detect somatic HLA mutations since we have paired tumor and normal WES or RNA…
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This concept is currently being used out in the wild but is not found in the schema. It seems sufficiently useful, and no term of same meaning already exists in schema.
Recommendation: ?