Hi there,

I have a contig that I’d like to remove from a bam file. I have tried removing it using picard and samtools but the darned thing is still in there.

This is what I’ve tried:

Step 1: create list of contigs I’d like to keep/remove

Keep:

samtools idxstats sampleID_markedup.bam | cut -f 1 | grep -v name_of_contig  > toKeep.txt

Remove:

cat > offendingContig.txt
name_of_contig

Step 2: Remove offending contig

Picard

Method 1: keep all but offending contig

java -jar $picard FilterSamReads I=sampleID_markedup.bam O=sampleID_trim.bam READ_LIST_FILE=toKeep.txt FILTER=includeReadList

Method 2: explicitly exclude contig

java -jar $picard FilterSamReads I=sampleID_markedup.bam O=sampleID_trim.bam READ_LIST_FILE=offendingContig.txt FILTER=excludeReadList

Samtools

samtools view -b -R toKeep.txt sampleID_markedup.bam > sampleID_trim.bam

For each method I don’t get any error messages (exit status zero and nothing written to error log), and a new .bam file is generated, but the contig is always still in there, which I check by using:

samtools view sampleID_trim.bam name_of_contig  | head -1 

Is the fact that the .bam file has already been marked for duplicates a possible issue?

Any help would be greatly appreciated.

Kind regards