wangnan9394/Sniffles_vcf_2_vg_vcf

output from Sniffles and filter with read by vg input

Sniffles_vcf_2_vg_vcf

obatin output from Sniffles and filter with read by vg input

purpose

get PAVs in your genome from pacbio_mapping_vcf(NGMLR+Sniffles), and merge the vcfs into vg to build a graphical based genome.

dependencies

environment：

path.os

vg https://github.com/vgteam/vg

samtools https://github.com/samtools/samtools

ngmlr https://github.com/philres/ngmlr

sniffles https://github.com/fritzsedlazeck/Sniffles

steps

preparation of input

mapping

ngmlr -t 8 -r GENOME -q FASTA -o SAM
samtools sort -O BAM -@ 20 -o BAM SAM &

calling

sniffles -t 8 -m BAM -v VCF

obatin output from Sniffles and filter with read by vg input

python Sniffles_vcf_2_vg_vcf.py -i VCF -g GENOME -p all/noraml/sort/clear -tmp 0/1

outputs

-tmp 0:local dir
-tmp 1:In a workdir "name"
-p all noraml+sort+clear
-p normal only normal
-p sort only sort(including reduce)
-p clear only clear

*.normal.sort.reduce.vcf

is the final vcf, for a further analysis.