Problems removing specific contig from .bam file

Question

[USA_225478]

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

Answer 1

[Pierre Lindenbaum]

 samtools view in.bam `samtools idxstat in.bam | cut -f1 | grep -E -v '^(chr2|\*)$'`

[USA_225478]

Hi Pierre, sorry for the late reply I've been off work for a few days.

Thank you so much, this works perfectly!

[Pierre Lindenbaum]

cool. Please, validate my answer (green tick on the left)

[USA_225478]

I tried to do that yesterday but the green tick appears to be missing!

[Pierre Lindenbaum]

enlarge your screen. https://imgur.com/8nvX23z

[marco.gabrielli94]

I've tried this using it, but I get an error saying that the command list is too long;

samtools view sample_4.sorted.bam `samtools idxstat sample_4.sorted.bam | cut -f1 | grep -E -v '^(prok_GCA_000243075.1_CP003171.1_from_11_to_747_total_737|\*)$'`
-bash: /usr/local/pace-apps/manual/packages/samtools/1.14/intel-19.0.5/bin/samtools: Argument list too long

sample_4.sorted.bam is the name of the bam file from which i need to remove the contig named "prok_GCA_000243075.1_CP003171.1_from_11_to_747_total_737".

What am I doing wrong?