This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Why bcftools gives (Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid)

I'm using Command: 

bcftools call -m -O v /10248_S4_L001_R1_001Sorted.vcf > /10248_S4_L001_R1_001SortedComplete.vcf

bcfToolsComplete Processing ended at: 2018/07/13 12:01:26 Result = 0
bcftools
Version: 1.8 (using htslib 1.8)

But befor 7-8 months I was getting

 Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid

Now I'm getting below note during execution

 Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid

Can someone explain the issue below-->? Is it affect output? & What the reason I'm getting these different NOTE over same CMD and Files?

genome sequence snp
• 5,324 views • link
written by soumyadas755 • soumyadas755

1 answer 

$ bcftools call

       --ploidy <assembly>[?]      predefined ploidy, 'list' to print available settings, append '?' for details
       --ploidy-file <file>        space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY
        -S, --samples-file <file>       PED file or a file with an optional column with sex (see man page for details) [all samples]

bcftools use those informations to know where it should expect a haploid region for a sexual chromosome.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre Lindenbaum, I update my question, Can you please look into it? Any Idea

• 1 views • link
written by soumyadas755 • soumyadas755

Log in to answer this question.

More posts like this