No variants found ( have problem in the handbook)
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7 weeks ago
quanyu • 0

I am new in bioinformatics. Today I was studying variation calling fllowing "the biostars handbook", when I found a bug out of my knowledge. Here is my code which is almost the same with the book chapter 87 : Variant calling example.

# Get the reference sequence.
efetch -db nuccore -format fasta -id $ACC | seqret -filter -sid$ACC > REF # Index reference for the aligner. bwa indexREF

# Index the reference genome for IGV
samtools faidx $REF # Get data from an Ebola sequencing run. fastq-dump -X 100000 --split-files$SRR

R1=${SRR}_1.fastq R2=${SRR}_2.fastq

# Align and generate a BAM file.
bwa mem $REF$R1 $R2 | samtools sort >$BAM

# Index the BAM file.
samtools index $BAM # Determine the genotype likelihoods for each base. bcftools mpileup -Ov -f$REF \$BAM > genotypes.vcf

# Call the variants with bcftools.
bcftools call --ploidy 1 -vm -Ov genotypes.vcf > variants1.vcf


When I view the resulting VCF file in IGV, I got "No variants found":

I can tell that my igv is good, that is I think it's the problem caused by other reasons. Good wishes for you!

bcftools handbook variation_calling igv • 284 views
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Appears as if you are using the wrong reference to view the data in IGV. Can you confirm that Handbook asks you to use AF08633 as the reference?

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I can guarantee it!