a collection of handy scripts

bioinformatics-scripts

# handy scripts for bioinformatics
# A collection of scripts that I find useful.

## convert bam to cram format

# define reference genome (required for cram format)
# GENOME="/data/publicData/genomes/human/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna" # hg38
GENOME="/data/publicData/genomes/human/GRCh37/hs37d5.fa" # hg19
# find all bam files in current dir and convert to cram
find . -name "*.bam" | sed "s/\.bam$//" | xargs -I {} -P 36 samtools view -@ 4 -T $GENOME -C -o {}.cram {}.bam
# index
find . -name "*.cram" | xargs -I {} -P 36 samtools index -@ 4 {}