Question: Why bcftools gives (Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid)
0
gravatar for soumyadas755
9 months ago by
soumyadas7550 wrote:

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?

snp sequence genome • 489 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by soumyadas7550
0
gravatar for Pierre Lindenbaum
9 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:
$ 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.

ADD COMMENTlink written 9 months ago by Pierre Lindenbaum119k

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

ADD REPLYlink written 9 months ago by soumyadas7550
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