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Variant calling using samtools
written by Chris 36Hi all, I modified my output as a vcf file but not bcf as the instruction. Is that OK or the output is not correct? …
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Why does bcftools call from different max-depth (-d) value in mpileup give inconstant GT values?
written by magnolia 3Hi, 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 4Why 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 Hans 15Hello 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 Ric 44Hi, 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 Ric 44Hi, 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 3Hi 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_sabiers 11I 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 AP 10Hello, 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 sacha 250I 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.