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This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode characters # Source: https://lh3.github.io/2021/07/06/remapping-an-aligned-bam samtools collate -Oun128 in.bam | samtools fastq -OT RG,BC - \ | bwa mem -pt8 -CH <(samtools view -H in.bam|grep ^@RG) ref.fa - \ | samtools sort -@4 -m4g -o out.bam - This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode characters # get header from first file and drop it from other files awk 'NR == FNR || FNR > 1' *.tsv > ${output_file} # Add a column for filename and filename column awk -v OFS='\t' 'NR == FNR { print \$0, 'filename' } FNR > 1 { print \$0, FILENAME }' This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode characters # This quick script will check for big differences in a bams index and creation date and perform indexing. for i in *.bam; do bam=${i} bai=${i}.bai bam_date=$(stat -c %Y ${bam}) bai_date=$(stat -c %Y ${bai}) diff=`expr ${bam_date} - ${bai_date}` if [ ${diff} -gt 100000 ]; then echo "${bam} ${diff}"; sbatch --job-name=${bam} --partition=cpu --time=3:00:00 --cpus-per-task=32 --wrap "samtools index -@ 32 ${bam}" This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode characters function split_bed() { # This function will split a bed file by chromosome and chunk_size=1000 # In other words, split files will only possess one chromosome max. # File sizes may be variable. awk -v chunk_size=1000 'NR == 1 { chrom=$1; iter=0; fname_iter=0; print chrom } { if(chrom == $1 && iter <= chunk_size) { print > sprintf("x%04d_%s.segment.txt", fname_iter, $1); iter++; } else { This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode characters resolve-symbolic-link() { if [ -L $1 ]; then temp="$(readlink "$1")"; rm -rf "$1"; cp -rf "$temp" "$1"; fi } This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode characters function node() { # Usage: # node ca015 # ssh into node and go to current directory ssh -t ${1} "cd ${PWD}; bash" } This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode characters #!/usr/bin/bash error() { >&2 echo -e "\n\t$(tput setaf 1)${1}$(tput sgr0)\n" exit 1 } msg() { >&2 echo -e "$(tput setaf 3)${1}$(tput sgr0)" } This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode characters # ITEMS <- vectorize(" # a # b # c # ") vectorize <- function(x) { x <- strsplit(x, "\n")[[1]] x[!is.na(x) & x != ""] } This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode characters parse_format_column <- df[, .(rbindlist( purrr::map2( strsplit(vcf_format, ":", fixed=TRUE), strsplit(vcf_gt, ":", fixed=TRUE), function(x, y) { names(y) <- x; data.table(t(y)) } ) ) ), ] This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode characters docker stop $(docker ps -a -q) docker rm $(docker ps -a -q)
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