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Created 2015-04-28 15:14:42 | Updated 2015-04-28 15:15:42 | Tags: vcf fasta format-convert
Comments (3)

Hello GATK Team,

Is there a tool within GATK that takes a multiple sequence alignment in FASTA format and converts to VCF? If not, could anyone point me to a tool that could do this task?

Many thanks, Nick

Created 2014-07-30 13:26:04 | Updated | Tags: fasta bam-files
Comments (3)


I am a phd student working in Sweden, currently trying to apply NGS data to phylogenetics.

I would like to know if there is a way to convert a sorted BAM file into a fasta sequence using only the mapped reads, i.e., without incorporating any of the reference into the fasta sequence?

I have sorted bam files that result from mapping reads of one species to a reference of a different species. Right now I am extracting the reads from the bam files and re-assembling them, but the result is sub-optimal because I often get multiple contigs, probably due to low coverage portions in the bam file, and this causes many alignment problems. I would like to get a single contig, perhaps with gaps inserted where there are no reads to match the reference, which would be much easier to align to other samples.

Regards, Filipe de Sousa