issues
search
cancerit
/
PCAP-core
NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)
GNU General Public License v2.0
9
stars
10
forks
source link
Feature/full read collate
#58
Closed
keiranmraine
closed
4 years ago
keiranmraine
commented
4 years ago
Base image updated to Focal (Ubuntu 20.04).
Majority of biobambam2 replaced with samtools functions.
Reads undergo full collate when mapping from BAM/CRAM (bwa-mem2 prep).
Duplicate marking
samtools markdup --mode
options exposed to
bwa_mem.pl
.
Scramble option for
bwa_mem.pl
deprecated, relevant option for fast CRAM random access exposed.
samtools markdup --mode
options exposed tobwa_mem.pl
.bwa_mem.pl
deprecated, relevant option for fast CRAM random access exposed.