Description

DeepSomatic is an extension of deep learning-based variant caller DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and normal data, produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports somatic variants in a standard VCF or gVCF file.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

4 ()

0 ()

1 ()

0 ()

1 ()

0 ()

1 ()

0 ()

1 ()

Output

Name
Description
Pattern

vcf ()

vcf_tbi ()

gvcf ()

gvcf_tbi ()

versions ()

Tools

deepsomatic Documentation

doi: 10.1101/2024.08.16.608331License: BSD-3-clause
Authors