Picky get fewer SV counts than sniffles when use minimap2 do the alignment

[PengJia6]

Hi,

I am trying to use picky to call SV for whole human genome with nanopore data which sequencing coverage is about 100X.
First, I use the minimap2 to do the aligment, and than I use the picky and sniffles to call SV.
Finally, I get 2117 SVs from picky call while 53357 from sniffles. I am very confused about it, could you please give me some advice about it. My script is as follow:

minimap2 alignment
###################################################
export PATH=/home/pengjia/anaconda3/bin:$PATH
thread=24
sample=blood36
thread=12
ref=/home/REF/GRCh38.d1.vd1.fa
bam=home/alignment/minimap2_result/${sample}_minimap2_sorted.bam
fastq=/home/fastq/${sample}.fastq.gz
minimap2 -a --MD -t $thread $ref $fastq | samtools view -@ $thread -Sb - | samtools sort -@ $thread -m 10G -o $bam
samtools index -@ $thread $bam
####################################################

pickly call SV based on minimap2 alignment bam
####################################################
export PATH=/home/pengjia/anaconda3/bin:$PATH
export PICKY=/home/pengjia/mysoftware/Picky/src/picky.pl
sample=blood36
thread=12
ref=/home/REF/GRCh38.d1.vd1.fa
bam=home/alignment/minimap2_result/${sample}_minimap2_sorted.bam
vcf=/home/SVCalling/minimap2_picky/out/${sample}_minimap2_picky_raw.vcf
prefix=/home/SVCalling/minimap2_picky/out/${sample}_minimap2_picky
samtools view -@ $thread -h $bam |tail -n +2| ${PICKY} sam2align | ${PICKY} callSV --oprefix $prefix
${PICKY} xls2vcf --xls ${prefix}.profile.DEL.xls --xls ${prefix}.profile.INS.xls --xls ${prefix}.profile.INDEL.xls --xls ${prefix}.profile.INV.xls --xls ${prefix}.profile.TTLC.xls --xls ${prefix}.profile.TDSR.xls --xls ${prefix}.profile.TDC.xls > $vcf
####################################################

Thanks,

Peng Jia