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hi sir:
there are many indel hotspot discovery in the paper of "Accelerating discovery of functional mutant alleles in cancer" as below:
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We identified 1,165 statistically si…
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We are running joint-discovery-gatk4 in slurm with Cromwell 46.
Only a small fraction of the shards are being processed concurrently.
What adjustments can be made to process more or all shards …
ghost updated
4 years ago
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I am experiencing a 26% false discovery rate (FDR) on the DREAM dataset 3 for indels only.
I run the tool with default parameters using the "paired variant calling" command from the documentation. For…
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Hello Alex,
I want to detect germline variant using GATK as it's described in this pipeline (https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indel…
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[GA00_AO2_BB1_01_annotsv_new.bed.zip](https://github.com/user-attachments/files/17144001/GA00_AO2_BB1_01_annotsv_new.bed.zip)
@lgmgeo Hello, I am trying to use the web version of annotsv, and I appr…
lpsyy updated
1 month ago
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HaplotypeCaller
Call germline SNPs and indels via local re-assembly of haplotypes
Overview
The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplot…
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Hello,
Thanks for such a great package!
In the `genomic_distribution` function, I understand that the expected amount of mutations for a region of interest is calculated as
`n_muts / surveyed…
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Hi，
I am using Pindel to call indels in our samples, Our samples are tumor-normal samples, and it's target sequencing data, the library was constructed by capturing.
I used BWA mem to map the tr…
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This subworkflow will cover the gatk4 best practices workflow: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- starting with the analys…
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