doFasta misses indels

[PAMorin]

I'm using doFasta -2 to extract the consensus sequence from bwa alignment (bam) files (for mitochondrial genomes). I've found that if there is a variable length repeat, ANGSD always generates the longer sequence even if most of the reads have the shorter repeat (e.g., if most are CCC, but a few are CCCC, the consensus is always CCCC). I think this is because ANGSD only counts the number of A, C, G, or T occurrences at the location, and ignores the indel "-" in the bam file. Is there a way to refine the bam alignment or otherwise use ANGSD doFasta to recognize indels?

[aalbrechtsen]

Dear PAMorin

ANGSD cannot generate a FASTA file based on the reference genome that is provided. So unfortunately it cannot include indels in the FASTA file.

-Anders

[ekg]

I believe you can use bcftools consensus to also handle indels.

On Sun, Jun 30, 2019, 07:35 Anders Albrechtsen notifications@github.com wrote:

Dear PAMorin

ANGSD cannot generate a FASTA file based on the reference genome that is provided. So unfortunately it cannot include indels in the FASTA file.

-Anders

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[PAMorin]

Thanks. I am starting to use the bcf approach, as described at: https://samtools.github.io/bcftools/howtos/consensus-sequence.html. It appears to be doing a good job at calling indels around variable repeats.

Phil

On 6/30/19 1:54 PM, Erik Garrison wrote:

I believe you can use bcftools consensus to also handle indels.

On Sun, Jun 30, 2019, 07:35 Anders Albrechtsen notifications@github.com wrote:

Dear PAMorin

ANGSD cannot generate a FASTA file based on the reference genome that is provided. So unfortunately it cannot include indels in the FASTA file.

-Anders

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Phillip A. Morin, Ph.D. Southwest Fisheries Science Center 8901 La Jolla Shores Dr. La Jolla, CA 92037, USA Phone: 858-546-7165 Fax: 858-546-7003 phillip.morin@noaa.gov http://swfsc.noaa.gov/mmtd-mmgenetics

[ekg]

As for calling indels, I'm not sure how good bcftools is. But it does have the tool to generate the consensus.

On Tue, Jul 2, 2019, 20:00 Phillip Morin notifications@github.com wrote:

Thanks. I am starting to use the bcf approach, as described at: https://samtools.github.io/bcftools/howtos/consensus-sequence.html. It appears to be doing a good job at calling indels around variable repeats.

Phil

On 6/30/19 1:54 PM, Erik Garrison wrote:

I believe you can use bcftools consensus to also handle indels.

On Sun, Jun 30, 2019, 07:35 Anders Albrechtsen <notifications@github.com

wrote:

Dear PAMorin

ANGSD cannot generate a FASTA file based on the reference genome that is provided. So unfortunately it cannot include indels in the FASTA file.

-Anders

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