Mercurial > repos > kyost > atac_primer_tool
comparison filter_bam.bash @ 0:fd3ea97a96bc draft
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
| author | kyost |
|---|---|
| date | Sat, 28 Apr 2018 15:07:26 -0400 |
| parents | |
| children | 3cd53127a838 |
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| -1:000000000000 | 0:fd3ea97a96bc |
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| 1 #Requires bam files and bed file containing coordinates of peaks of interest | |
| 2 #Generates filtered bams and library size file to upload into Galaxy | |
| 3 | |
| 4 #required arguements: | |
| 5 #($1): bam file | |
| 6 #($2): bed file containing regions of interest | |
| 7 | |
| 8 #Usage: filter_bam /pathtofolder/ qPCR_peaks.bed | |
| 9 | |
| 10 #outputs: | |
| 11 #Filtered bam files containing reads in regions of interest | |
| 12 #read_counts: txt file containing number of mapped reads in each bam file, used for normalization | |
| 13 | |
| 14 bam_file=$1 | |
| 15 peak_file=$2 | |
| 16 chrom_sizes=$3 | |
| 17 ext_peak_file=$4 | |
| 18 filtered_bam_file=$5 | |
| 19 read_counts=$6 | |
| 20 name=$7 | |
| 21 | |
| 22 bedtools slop -i $peak_file -g $chrom_sizes -b 2000 | sort -k1,1 -k2,2n - > $ext_peak_file | |
| 23 | |
| 24 samtools index $bam_file | |
| 25 | |
| 26 samtools view -c -F 1284 $bam_file > count | |
| 27 echo $name > name | |
| 28 paste name count > $read_counts | |
| 29 | |
| 30 #create bed file of fragments for each bam file | |
| 31 | |
| 32 samtools view -b -L $ext_peak_file $bam_file > $filtered_bam_file | |
| 33 | |
| 34 rm name | |
| 35 rm count |