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-   -   I cannot detect a deletion which is seen by IGV (http://seqanswers.com/forums/showthread.php?t=77707)

muratisbilen 08-23-2017 03:25 AM

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,

gringer 08-23-2017 03:30 AM

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.

Brian Bushnell 08-23-2017 09:43 AM

I'd suggest trying a different variant caller. The one I wrote (callvariants.sh in the BBMap package) works very well for calling indels from Illumina data, in terms of concordance with what you see in IGV.

muratisbilen 09-05-2017 03:43 AM

Thanks guys but neither of them worked. callvariants.sh 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?

Regards,

finswimmer 09-07-2017 09:22 PM

Hello,

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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