Multisamples in callvariants with callvariants.sh

Question

[Hayler Edu]

Hello

Yesterday I did a variant calling with 132 samples using callvariants.sh but the problem is that in the vcf file, I can't differentiate which SNPs belong to which sample.

I use the parameter sample but the name of the samples only appeared in the header of the file.

It's possible to create a VCF file with the 132 samples and the SNPs of each sample differ.

Thanks

[Ram]

Please provide feedback and/or closure to your previous posts:

• Improve coverage in callvariants.sh
• Variables in for loop
• Mapping with bbmap.sh
• Alignment with bbmap.sh
• Start Using conda
• Error in dyn.load(file, DLLpath = DLLpath, ...) :
• I don't find trimmomatic.jar file

Do not keep opening new posts without following up on older posts - that is really bad etiquette; we are not your paid personal consultants.

[GenoMax]

If you had used multiple files as input for the tool then you should have got an output with the following format (from help):

In multisample mode, each file is treated as an individual sample, and gets its own column in the VCF file. Unless overridden, input file names are used as sample names.

[Hayler Edu]

When I use the multisample mode I have a problem because when I get the VCF file the names of the sample doesn't appear in the column

This is my pipeline:

callvariants.sh in=pimm1_PyMag26_il.fastq.sam,pimm1_PyMag25_il.fastq.sam,pimm1_PyMag14_il.fastq.sam out=VCF3.vcf ref=GCF_001660625.2_IpCoco_1.2_genomic.fna multisample=pimm1_PyMag26_il.fastq.sam,pimm1_PyMag25_il.fastq.sam,pimm1_PyMag14_il.fastq.sam

java -ea -Xmx79966m -Xms79966m -cp /home/bioinformatica/miniconda3/envs/bbtools/bbtools/lib/current/ var2.CallVariants in=pimm1_PyMag26_il.fastq.sam,pimm1_PyMag25_il.fastq.sam,pimm1_PyMag14_il.fastq.sam out=VCF3.vcf ref=GCF_001660625.2_IpCoco_1.2_genomic.fna multisample=pimm1_PyMag26_il.fastq.sam,pimm1_PyMag25_il.fastq.sam,pimm1_PyMag14_il.fastq.sam

Executing var2.CallVariants [in=pimm1_PyMag26_il.fastq.sam,pimm1_PyMag25_il.fastq.sam,pimm1_PyMag14_il.fastq.sam, out=VCF3.vcf, ref=GCF_001660625.2_IpCoco_1.2_genomic.fna, **multisample=pimm1_PyMag26_il.fastq.sam,pimm1_PyMag25_il.fastq.sam,pimm1_PyMag14_il.fastq.sam]**

Something is wrong?

Answer 1

[GenoMax]

You need to run

callvariants.sh in=pimm1_PyMag26_il.fastq.sam,pimm1_PyMag25_il.fastq.sam,pimm1_PyMag14_il.fastq.sam out=VCF3.vcf ref=GCF_001660625.2_IpCoco_1.2_genomic.fna multisample=t

Multi-sample option does not accept names of samples.You simply set to to true.

You could provide names with sample=Sample1,Sample2... This should not be required since your file names will be used as sample names.

[Hayler Edu]

Thanks that script solve my problem with the samples

[GenoMax]

Please accept the answer to provide closure to this thread (green check mark).