This repository stores custom WDLs for our project analyzing data using the Terra platform.
#Extracting reads previously mapped to GRCh38.
(1) Converting CRAM files to BAM files (samtools, CRAM-to-BAM_multithreaded.wdl).
(2) Stripping reads from the BAM files, pairing them and trimming them, with QC (samtools, bbmap, and trim_galore, StripReadsFromBams.wdl).
#Map trimmed reads to new genome assembly (CHM13).
(3) Convert paired fastqs to CRAM files (bwa and sam
This is a companion discussion topic for the original entry at github.com/DrPintoThe2nd/XYalign_AC3/CRAM-to-BAM