Question: How To Extract Consensus Sequence Of Mapped Regions From A Bam File?
3
gravatar for lin.barnum
6.1 years ago by
lin.barnum230
lin.barnum230 wrote:

I would like to extract consensus sequence of only the mapped regions from a BAM file. I have a bam file which contains only a few regions that are mapped, most of my regions are completely unmapped. How could I go about this?

Thanks,

bam samtools • 7.3k views
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 6.1 years ago by lin.barnum230
2

You might find this thread or this link useful for your purpose.

How to generate a consensus fasta sequence from SAM tools pileup?

http://chipster.csc.fi/manual/samtools-consensus.html

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by toni2.1k
2
gravatar for bioinfo
6.1 years ago by
bioinfo690
EU
bioinfo690 wrote:

FastaAlternativeReferenceMaker function from picardtools compares variant files to reference to create a consensus fasta sequence ; -L flag takes the input intervals file, -o flag gives the output consensus fasta file, -variant flag takes the variant file (SNPS and Indels together) -R flag takes the reference genome

java -Xmx2g -jar /GATK_pre/GenomeAnalysisTK-1.0.4905/GenomeAnalysisTK.jar -R reference.fasta -T FastaAlternateReferenceMaker -L sorted.bam.intervals -o consensus.fasta –variant snps_indel_file
ADD COMMENTlink written 6.1 years ago by bioinfo690
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