VNTRSeek is a computational pipeline for the detection of VNTRs in short read sequencing data. It was developed by Yevgeniy Gelfand, Yozen Hernandez, and Gary Benson, with contributions from Marzie Rasekh, and more recently streamlined by Kyler Anderson in the Benson Lab for Biocomputing and Informatics at Boston University.
Add an extra option, required when processing CRAM files, for specifying the reference file.
This feature will require a new function for handling CRAM files, but no new dependencies.
Samtools command invocation should look something like: samtools view -T $cram_ref ..., where ... is the rest of the options already given in the existing SAM/BAM file code.
Add an extra option, required when processing CRAM files, for specifying the reference file.
This feature will require a new function for handling CRAM files, but no new dependencies.
Samtools command invocation should look something like:
samtools view -T $cram_ref ..., where...is the rest of the options already given in the existing SAM/BAM file code.