I would like to get some summary statistics on a vcf file from one individual, which has over a million variant calls. I've tried to make a histogram of indel sizes with this command,
vcftools --vcf sample.vcf --out sample --hist-indel-len
but it returns an empty file. I see thousands of deletions in the vcf, although strangely no insertions. A typical line in the vcf file I have looks like
NC_025968.3 168363 191 N <DEL> . . SVTYPE=DEL;STRANDS=+-:19;SVLEN=-1026;END=169389;CIPOS=-9,330;CIEND=-152,9;CIPOS95=-3,61;CIEND95=-32,3;IMPRECISE;SU=19;PE=19;SR=0 GT:SU:PE:SR ./.:19:19:0
Update: I aligned reads to my reference with BWA MEM, then used samblaster to extract discordant pairs and split-reads. I sorted and indexed the three bam files, then used lumpyexpress to generate the vcf.
samblaster -i sample.sam --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 | samtools view -S -b - > sample.bam samtools view -h sample.bam | samblaster -a -e -d sample.disc.sam -s sample.split.sam -o /dev/null lumpyexpress -B ../sample.sorted.bam -S ../sample.split.sorted.bam -D ../sample.disc.sorted.bam -o sample.vcf
I would like to see the size distribution of deletions, and if possible, figure out why there are no insertions.