consensus

[ldutoit]

Hi Alana,

let's be fancy and use the issues tool :)

for the consensus, after filtering of duplicated, I ended up using this:

https://github.com/samtools/bcftools/wiki/HOWTOs#consensus-calling under section consensus calling... (Note this is not my github). you can also use --ploidy 1 for mitochondrial sequence in bcftools call.

Coment welcome if you think this is inappropriate!

Cheers

Ludo

[ldutoit]

Here is the small script I use in case it is of any use. It is made to work on Nesi.

cheers

Ludo

MakeConsensus.sh.zip

[laninsky]

Awesome, cheers Ludo! Do you mind if I add this script in to this repository? I think this is a good work around, but I am also curious about how the --ploidy 1 flag will handle your heteroplasmic sites. Do you reckon it will just call the majority base? I think I reinvented the wheel over at https://github.com/laninsky/direct_mito_sequencing/tree/master/4_filtering_fasta_on_pileup by doing a similar thing from the pileup too :)

[ldutoit]

Please do! I spend my days reinventing the wheel :)

Yeah, it probably call the majority base but it is also easy to tweak it towards a diploid call with 😃 by removing --ploidy 1 in the bcftools call.

Always possible can also look at the output of the bcftools call which is a vcf if you want to do more fancy stuff.

Note that the module load part of the script is specific to Nesi.

cheers