Hello, author, I followed the svtools process to talk about lsort and lmerge of multiple vcf files, and then I used svtools for genotyping and annotated their copy numbers, and then I pasted the annotated cn.vcf through vcfpaste, but when I looked at the gt.cn.vcf file, There will be such an error: "[e:: vcf parse format] incorrect number of format fields at NW _ 026258581.1: 13116",
My orders are as follows:
svtools lsort --vcf-list lsort.list > 82.lsort.vcf；
At this step, an error will appear: "e:: vcf parse format] incorrect number of format fields at NW _ 026258581.1: 13116.
[E::vcf_parse_format] Incorrect number of FORMAT fields at NW_026259125.1:2470
Error: VCF parse error”
Hello, author, I followed the svtools process to talk about lsort and lmerge of multiple vcf files, and then I used svtools for genotyping and annotated their copy numbers, and then I pasted the annotated cn.vcf through vcfpaste, but when I looked at the gt.cn.vcf file, There will be such an error: "[e:: vcf parse format] incorrect number of format fields at NW _ 026258581.1: 13116", My orders are as follows: svtools lsort --vcf-list lsort.list > 82.lsort.vcf；
svtools lmerge -i 82.lsort.vcf -f 20 > 82.lmerge.vcf；
cat 82.lmerge.vcf | vawk --header '{ $6="."; print }' | svtools genotype -B ${sample}.rmdup.bam -l ${sample}.json | sed 's/PR...=[0-9.e,-]*(;){0,1}(\t){0,1}/\2/g' - > ${sample}.gt.sv.vcf；
svtools copynumber --cnvnator cnvnator -s ${sample} -w 1000 -r ${sample}.root -c coordinates -i ${sample}.gt.sv.vcf > ${sample}.cn.vcf； ls *.cn.vcf >cn.list svtools vcfpaste -m 82.lmerge.vcf -f cn.list -q > merged.gt.cn.vcf; bcftools view -H merged.gt.vcf|wc -l
At this step, an error will appear: "e:: vcf parse format] incorrect number of format fields at NW _ 026258581.1: 13116. [E::vcf_parse_format] Incorrect number of FORMAT fields at NW_026259125.1:2470 Error: VCF parse error”