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

Join Date: Aug 2017
Posts: 2
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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