No sample in the VCF file!
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6 days ago
ebhmayra • 0

Hi guys,

Can you please help me with this. I am working with trying to do:

vcf.fn <- "sequences_covid_SRA_april21_36genomes_sequence_aligned.trimmed.fasta.vcf" 
snpgdsVCF2GDS(vcf.fn, "sarscov2.gds", method="biallelic.only")

and I got this error:

No sample in the VCF file!

Which could be the reasons for this error? I check the file and it seems ok. Thank you in advance.

VCF VCFR • 104 views
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what is the output of

grep "#CHROM" -m1 sequences_covid_SRA_april21_36genomes_sequence_aligned.trimmed.fasta.vcf

If it is only #CHROM POS ID REF ALT QUAL FILTER INFO , then there is no sample in the vcf.

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What is the output to the shell command:

bcftools query -l sequences_covid_SRA_april21_36genomes_sequence_aligned.trimmed.fasta.vcf

You'll need to have bcftools installed to run the above command. If it's not installed, give us the output to:

grep -m1 -E "^#CHROM" sequences_covid_SRA_april21_36genomes_sequence_aligned.trimmed.fasta.vcf | tr "\t" "\n"
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