Question: How Reads Have Been Mapped In My Bam File?
0
gravatar for Pascal
7.7 years ago by
Pascal1.5k
Barcelona
Pascal1.5k wrote:

Working with 1000 Genome Project bam files (NA12878, pilot2), I'd need to know how the reads have been mapped and in particular if there are "unique mapping" for all these reads or if reads have multiple possible mapping.

alignment bam • 2.0k views
ADD COMMENTlink written 7.7 years ago by Pascal1.5k
1
gravatar for toni
7.7 years ago by
toni2.1k
Lyon
toni2.1k wrote:

Are there any @PG lines in your BAM file header?

samtools view -H file.bam | grep "^@PG"

This displays only the @PG lines of the header; if any.

I have downloaded NA12878 once from the Broad and it seems that the the answer is 'bwa 0.5.7' GATK realigner seems to have been used as well.

And if it was indeed mapped with BWA you can check for the 'X0' and 'X1' tag in the alignment (if present, number of best hits ans suboptimal hits respectively)

ADD COMMENTlink written 7.7 years ago by toni2.1k

No @PG in header. I had verified this point already. Thanks anyway.

ADD REPLYlink written 7.7 years ago by Pascal1.5k

Regarding the X0, X1, this is a very good idea, but unfortunately it does not seem to be present (I assume, according to SAM format specifications that "X0" or "X1" might be present): samtools view NA12878.chrom1.SLX.maq.SRP000032.2009_07.bam | grep X0

ADD REPLYlink written 7.7 years ago by Pascal1.5k
1
gravatar for Vikas Bansal
7.7 years ago by
Vikas Bansal2.3k
Berlin, Germany
Vikas Bansal2.3k wrote:

I think NA12878 was sequenced using Illumina and mapped by bwa with following commands->

bwa index -a bwtsw $ref (where $ref is the reference fasta file)
bwa aln -q 15 $ref $fq > $sai
bwa samse $ref $sai $fq > $bam

You can find the information in section B Alignment Process, here.

ADD COMMENTlink written 7.7 years ago by Vikas Bansal2.3k
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