How to specify samples for GATK FastaAlternateReferenceMaker in the option --use-iupac-sample

Question

[b03601015]

I'm now trying to create a fasta file that contains consensus sequences of multiple samples (for multiple sequence alignment) from a multiple sample vcf file. I tried the following, but it failed to recognize my samples.

gatk FastaAlternateReferenceMaker --output 20210124quinoa_Cq1A.fa -reference /pfs/work7/workspace/scratch/ho_chuang-data-0/ref/quinoa_ref_V2_Cq1A.fa --variant quinoas_Cq1A.vcf.gz --use-iupac-sample S2H1_NKD181100721_H7VJJDSXX_L2,SRR4300210,SRR4300211,SRR4300212,SRR4300213,SRR4300214,SRR4300215 and --use-iupac-sample [S2H1_NKD181100721_H7VJJDSXX_L2,SRR4300210,SRR4300211,SRR4300212,SRR4300213,SRR4300214,SRR4300215] and --use-iupac-sample {S2H1_NKD181100721_H7VJJDSXX_L2,SRR4300210,SRR4300211,SRR4300212,SRR4300213,SRR4300214,SRR4300215} and --use-iupac-sample "S2H1_NKD181100721_H7VJJDSXX_L2,SRR4300210,SRR4300211,SRR4300212,SRR4300213,SRR4300214,SRR4300215"

But none of them worked. How should I list my samples so that the software could recognize it?

Answer 1

[Pierre Lindenbaum]

as far I can see, only one sample can be specified.

https://github.com/broadinstitute/gatk/blob/master/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker.java#L118

and

https://github.com/broadinstitute/gatk/blob/master/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker.java#L133

Answer 2

[Buxus]

An alternative is to maybe use bcftools consensus.