# Tagged with #fastaalternatereference 1 documentation article | 0 announcements | 4 forum discussions

Created 2012-07-23 23:55:38 | Updated 2012-07-23 23:55:38 | Tags: gatkdocs fastaalternatereference

A new tool has been released!

Check out the documentation at FastaAlternateReference.

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Created 2015-05-06 17:39:20 | Updated | Tags: fastaalternatereference

I specify my interval as 1-1527. The output does not align with position 1 of my (bacterial) reference genome, even though it is 1527 bp long. Position 1 of the output actually aligns with position 87 of my reference genome, and then skips one base about every 70bp (see attachment). I can't figure out what the problem is.

gatk.sh -Xmx2g -R /global/scratch/ahlstrom/ref_MAP4/MAP4.fasta -T FastaAlternateReferenceMaker -L WGreverse.intervals --variant /global/scratch/ahlstrom/MAP4_VCF/$1_MAP4.vcf -o WGreverse/$1_WGreverse1.fasta

Thanks, Christina

Created 2015-03-02 10:13:32 | Updated 2015-03-02 10:30:32 | Tags: fastaalternatereference fastaalternatereferencemaker

Hello, I really like yor FastaAlternateReferenceMaker to build a new consensus from FASTA+VCF. However, it deletes all headers from the FASTA file and replaces them by numbers. Is there a way to change this behavior, e.g. simply take the old headers?

Best, Boyke

Created 2013-09-27 13:49:14 | Updated | Tags: combinevariants haplotypecaller fastaalternatereference coverage

Hi, I'm calling Variants with HaplotypeCaller in a population of 2 Parents and 7 F1-individuals. After read backed phasing I'm combining the vcf files of my genotypes with CombineVariants. In the outfile I very often find "./.". I thought this means there is no coverage at a certain position. But at many positions I do have good coverage. Why do I then get ./.? Moreover I used FastaAlternateReferenceMaker and created a new reference sequence including the variants from the parents. In that case, after I run HC and do the phasing and combine variants steps, I only get "./." at positions where there is really no coverage (as I can see in my mappings). Nadia

Created 2012-10-11 08:18:08 | Updated 2012-10-18 01:25:50 | Tags: fastaalternatereference

Hi GATK team,

I have a VCF file (from GATK) containing variants for a total of 20 individuals and I'm wondering how to get the consensus sequences for each individual regarding its own polymorphism. Some individuals may not show polymorphism at a particular position in a contig whereas some others may. I've checked the GATK dedicated tool (FastaAlternateReferenceMaker) but it doesn't answer my question as only one consensus is generated. My requirement would be to get as many outputs files (containing consensus file) as mapped individuals.

Is there anyway to get this task achieved using GATK?

Thanks, C.