tanbiswas

Unreliable GISTIC2 results

1

Hi Initially I ran gistic2 on hiplot platform using 31 samples as an input. Where I got some amplified and deleted peaks. Later, I have added one more samples to...

How to normalise different sequencing coverage samples in CNVKit?

1

Hi I'm using CNVKit to identify copy number alterations using WES data. However, our tumor samples have a coverage of 200x and corresponding normal samples have a coverage of 100x....

CNVkit segment command RuntimeError: Subprocess command failed

5

I am using CNVkit to call somatic CNAs from tumor-normal paired WES data. The BAM files were generated using GATK pipeline and the somatic VCF file was called using Mutect2...

Dear Developers, Thank you for developing the cnv_facets. I am using FACETS to identify CNVs in my WES data. However, I have some queries regarding the output and how to...