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How does bcftools decide what sample name to assign when calling variants?
written by Paul •How does bcftools decide what sample names to assign in the vcf when performing variant calling using `mpileup` and `call` commands? I'm using bcftools to …
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Why does bcftools call from different max-depth (-d) value in mpileup give inconstant GT values?
written by magnolia •Hi, I want to call variants from a BAM file with bcftools. To use `call` command, I have to use `mpileup` command to create a …
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Why Does Mpileup Skip some variants ?
written by sami •Why Does Mpileup Skip some variants ? when I make variant call with bcftools mpileup and call , i can't get some variants,especially those have …
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Dinucleodite variants are marked at single nucleotide variant in BCFTOOLS CALL
written by HansHello I have generated a vcf file using bcftools pileup and bctools call using this code: `bcftools mpileup -Ou -f ref.fa in.bam | \ bcftools …
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Failed to open var.raw.bcf: unknown file type
written by RicHi, I used the following commands to call SNPs samtools merge ${1}/all.sorted.dedup.bam ${1}/*.sorted.dedup.bam samtools index ${1}/all.sorted.dedup.bam samtools faidx $2 samtools mpileup -uf $2 ${1}/all.sorted.dedup.bam | …
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Failed to open var.raw.bcf: unknown file type
written by RicHi, I used the following commands to call SNPs samtools merge ${1}/all.sorted.dedup.bam ${1}/*.sorted.dedup.bam samtools index ${1}/all.sorted.dedup.bam samtools faidx $2 samtools mpileup -uf $2 ${1}/all.sorted.dedup.bam | …
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Discrepancy between number of SNP calls using samtools/bcftools when --skip-indels flag used
written by TrentGenomics •Hi all, I've used the following command to call SNPs between two species: samtools mpileup -gf NFS_reference.fasta SFS_alignment_bowtie2.coordSorted.bam | bcftools call -Ou -mv | bcftools …
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direct call of indels/snps with bcftools?
written by cristina_sabiersI am wondering... With vcftools I can call directly my snps and indels from my vcf file, but with bcftools I only found this way …
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Empty VCF file with bcftools call
written by APHello, I am trying to produce a vcf file using bcftools call but it produces an empty vcf file containing only the header. In short, …
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What's the difference between mpileup output and bcftools call ?
written by sachaI guess it's a simple question.. Could you detail what's the difference between vcf file generated by samtools and from bcftools? ``` samtools mpileup - …
VCF files (and other files that contain records which are usually accessed at random) benefit from indexes the same way books do - it makes the lookup process faster as one knows exactly which memory location (like page number) to go to.