This repository stores custom WDLs for our project analyzing data using the Terra platform.

Step outlines:

#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

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