Extract reference and aligned sequences from BAM file basing on VCF file

[floem7]

I couldn't find relevant information. I hope it's not duplicate.

I have resequencing data for two maize lines (BAM and VCF files).
I want to extract sequences (fasta) for several genes (I have also GFF3 file with annotation data) from reference genome and corresponding sequences from resequencing data. I probably could use sequence identifiers, as they are in my files

Which tool allows to extract such data, and more generally to extract sequences for
a given variant type (SNP, indel, etc) and location (exon, intron, etc)?

[sarvidsson]

You can try

- "vcf-consensus" from VCFtools: http://vcftools.sourceforge.net/perl...#vcf-consensus. Click on "Read more" to get an example how to get the consensus for a given region within the reference sequence (you need to extract this information from your GFF).

or

- FastaAlternateReferenceMaker within GATK (https://www.broadinstitute.org/gatk/...renceMaker.php)

Read the documentation thoroughly - there are several caveats!

[sarvidsson]

Forgot to mention, if you just want to extract FASTA sequences for GFF features (i.e. without any called variants applied), you can use BEDTools getfasta (http://bedtools.readthedocs.org/en/l.../getfasta.html).

[floem7]

Thanks, I've followed example found at vcftools page and it works :-)

Great thanks!

Edit: however, I realized that aligned fasta format would be better. The aim is to quickly generate
friendly msa view for a given region. For example for primer design.

Certainly, ordinary MSA programs don't create sufficiently similar alignment as this in bam file.
So it require manual inspection.