samtools variant calling for separate chromosomes

[tahamasoodi]

Is there anyway to call variants separately for each chromosome (separate output files) using a single command in samtools. I am having whole genome data and when I annotate it using annovar, I'm getting a very big file which can not be loaded in excel, so I want a separate vcf file for each chromosome so that i can annotate them separately using annovar.

Thanks,

[tahamasoodi]

There seems to be no response for my query.

[tahamasoodi]

Can anybody help?

[Khen]

There is an example in the manual.

http://samtools.sourceforge.net/samtools.shtml
samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam

The '-r' argument allows you to specify the region.

[tahamasoodi]

This command will call variants separately for each chromosome thus we have to use 24 commands for 24 chromosomes. But, I want a single command to call variants for all the 24 chromosomes, each chromosome having a separate vcf file.

[tahamasoodi]

Can this be done in samtools?

[westerman]

No. Samtools will not output 24 individual files with a single command. Learn some shell scripting. It is easy enough to run 24 commands with a single shell command.

[tahamasoodi]

Then how can we view the WGS data as the single output vcf file of samtools after annotation in annovar is equal to around 900 MBs which cannot be viewed in excel?

[westerman]

Then how can we view the WGS data as the single output vcf file of samtools after annotation in annovar is equal to around 900 MBs which cannot be viewed in excel?

That question does not make sense when looking at your previous comments in this threads. Basically, if you need a single file with all chromosome variants in it then samtools/bcftools/vcfutils will provide this. Or if you need 24 individual files one per chromosome then samtools will provide this ... however you will either need to type in the samtools command 24 times (with slightly different parameters) or you will need to create a shell script that will run samtools 24 times.

Your very first question was "... so I want a separate vcf file for each chromosome ..." to which Khen provided the answer. You then asked, somewhat confusingly, "... Can this be done in samtools?" to which I took the word "this" to mean "generate 24 VCF files" which samtools can not do in a single command.

[swbarnes2]

NGS simply makes too much data for a person to deal with if all the tools they have are mindlessly copied command lines and Excel. You have to learn shell scripting, or Perl, or Python, or something to handle large text files.