bcftools for plant SNPs

Question

[Ric]

Hi, I ran bcftools in the following way:

bcftools mpileup -O b -o ${3}-${basename}.bcf -f $asm $bam 
bcftools call --ploidy 2 -m -o ${3}-${basename}.vcf ${3}-${basename}.bcf

for a plant genome with --ploidy 2. However, I got this message:

Note: The maximum per-sample depth with -d 250 is 125.0x

PRE-DEFINED PLOIDY FILES

 * Columns are: CHROM,FROM,TO,SEX,PLOIDY
 * Coordinates are 1-based inclusive.
 * A '*' means any value not otherwise defined.

GRCh37
   .. Human Genome reference assembly GRCh37 / hg19

GRCh38
   .. Human Genome reference assembly GRCh38 / hg38

X  
   .. Treat male samples as haploid and female as diploid regardless of the chromosome name

Y  
   .. Treat male samples as haploid and female as no-copy, regardless of the chromosome name

1  
   .. Treat all samples as haploid

Run as --ploidy <alias> (e.g. --ploidy GRCh37).
To see the detailed ploidy definition, append a question mark (e.g. --ploidy GRCh37?).

How can I increase the ploidy level?

Thank you in advance,

Answer 1

[Pierre Lindenbaum]

The option --ploidy is not defined to change the ploidy of the reference sequence as you can see in the manual. It's used to define the haploid (sexual) regions of the genome.

--ploidy 2

just like human. So you don't have to change the ploidy

[Ric]

What should I set for --ploidy value for plants?