比对

  3. minimap2 \
  4.   -x map-ont \
  5.   -t 4 \
  6.   --MD \
  7.   --cs \
  8.   -a \
  9.   ${ref} \
  10.   ${sample}.fq.gz \
  11.   | samtools sort - -o ${sample}.sort.bam

SV 检测

  1. sniffles \
  2.   -m ${sample}.sort.bam \
  3.   -v ${sample}.sniffles.vcf \
  4.   --min_support 5 \
  5.   --min_length 50 \
  6.   --threads 4 \
  7.   > ${sample}.sniffles.log
  9. awk '$1 ~ /#/ || ($7 != "STRANDBIAS" && $8 !~ "IMPRECISE" && $7 != "UNRESOLVED")' \
  10.   ${sample}.sniffles.vcf \
  11.   > ${sample}.sniffles.filter.vcf
  13. ls *.sniffles.vcf > vcf_raw_calls.txt
  15. SURVIVOR merge \
  16.   vcf_raw_calls.txt \
  17.   1000 1 1 -1 -1 -1 \
  18.   merged_1kbpdist.vcf

  1. sniffles \
  2.   -m ${sample}.sort.bam \
  3.   -v ${sample}.sniffles.gt.vcf \
  4.   --Ivcf merged_1kbpdist.vcf \
  5.   --min_support 5 \
  6.   --min_length 50 \
  7.   --threads 4 \
  8.   > ${sample}.sniffles.gt.log
  11. ls *.sniffles.gt.vcf > vcf_gt_calls.txt
  13. SURVIVOR merge \
  14.   vcf_gt_calls.txt \
  15.   1000 -1 1 -1 -1 -1 \
  16.   merged_1kbpdist.vcf

参考