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Old 08-23-2017, 04:25 AM   #1
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Location: Kocaeli

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Default I cannot detect a deletion which is seen by IGV

Hi everybody,

I use samtools and bcftools 1.4.1 for variant calling. However, I cannot detect deletions for a specific position. In fact, when I visualize my data in IGV (by Broad Institute) I can see an obvious heterozygous deletion from T to no nucleotide (52% T, 45% - , 3% others) at 3294155th position of chr16 (hg19). However, samtools and bcftools cannot detect this deletion. What could be the reason for that? How can I modify my code shown below to call this deletion?

samtools mpileup -ABuvf ~/Desktop/Analysis/hg19/hg19.fa ${outpath}/sortedBowtieOut.sam -o ${outpath}/mpileup.vcf

bcftools call -v -c -O v -o ${outpath}/sortedBowtieOut_samtools_raw_variants.vcf ${outpath}/mpileup.vcf

Thanks, Kind Regards,
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Old 08-23-2017, 04:30 AM   #2
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838

Samtools mpileup has its own INDEL correction, which may be influencing the results that you're seeing. You could try skipping this (option `-I) and seeing if it changes the results.
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Old 08-23-2017, 10:43 AM   #3
Brian Bushnell
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Location: Walnut Creek, CA

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I'd suggest trying a different variant caller. The one I wrote ( in the BBMap package) works very well for calling indels from Illumina data, in terms of concordance with what you see in IGV.
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Old 09-05-2017, 04:43 AM   #4
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Location: Kocaeli

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Thanks guys but neither of them worked. gives an out of memory error :/

To test the ability of bcftools to detect INDELs, I generated a dummy data, which includes 100 forward and 100 reverse reads. Among these, 50% of the paired reads have a deletion on a specific position. bcftools still cannot detect such a pure deletion. How can I use/change parameters to make bcftools call such indels?

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Old 09-07-2017, 10:22 PM   #5
Location: Europe

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can you post a screenshot of IGV in this region? If I found it correctly, this is a position in a homopolymer run (11xT) which is typical not easy to sequence, align and discover a variant.

As Brian suggested try out another variant caller. My favorite is freebayes.

fin swimmer
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