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Multisamples in callvariants with callvariants.sh

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

bbtools callvariants
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written by Hayler Edu • Hayler Edu

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.

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written by GenoMax GenoMax

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?

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updated by GenoMax GenoMax • written by Hayler Edu • Hayler Edu

1 answer

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.

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written by GenoMax GenoMax

Thanks that script solve my problem with the samples

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written by Hayler Edu • Hayler Edu

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

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written by GenoMax GenoMax

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