PLAF file

[trn30]

Hello,
I am trying to use DEploid with vcf files obtained through GATK and I don't know how to generate the PLAF file, I have tried to extract from the gatk vcf the AF value and generate a table as required but it generates this error:

Error: Number of sites was wrong (compares to ref count)

could you help me to solve this question or tell me how to generate the correct PLAF file?

[nramme]

I am also having this problem. Does anyone have a solution?

[shajoezhu]

dear @nramme and @trn30 , just saw your message,

please see this repo https://github.com/DEploid-dev/DEploid-Supplementary-Materials

I initialy filter the vcf file to high quality sites, extract the ref and alt counts for each sample, and you can compute the plaf by

PLAF = \sum_{ALT} / (\sum_{ALT} + \sum_{REF})

[trn30]

Thank you very much for your reply, I have followed your recommendations and got the plaf file but when I run deplod I get this error as a result:

"Error: Number of sites was wrong (compared to ref count) in: /mnt/beegfs/lab204/Pacbio_clones_0523/Phasing/variantcalling/demultiplex.bc2067_2068_30_70_merged_PLAF.txt"

The number of lines in the plaf file matches the number of lines validated in the vcf file. I have also added a header to the PLAF files containing "CHROM POS PLAF" separated by tabs al the rest of the rows.

I am very interested in using the program, so if you could help me to correct these errors and make it work I would be very grateful.

Thanks in advance.

[shajoezhu]

hi @trn30

The number of lines in the plaf file matches the number of lines validated in the vcf file

Do you know what is causing this?