Force calling

[lunky-zao]

When I use -Ivcf to force calling, there is no 'TRA' or 'BND' in my vcf files.
The command is :
nohup cuteSV A.sort.bam re.fasta A.cuteSV.vcf cutesv/ --threads 16 --sample A --retain_work_dir --report_readid --genotype --min_size 50 --max_size 100000 --min_support 4 --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 > cutesv.log &
ls *.out.cuteSV.vcf > all_level_calls.txt
SURVIVOR merge all_level_calls.txt 1000 1 1 -1 -1 -1 all_cohort_level.vcf > survivor.log &
nohup cuteSV A.sort.bam re.fasta A.cuteSV.vcf cutesv/ -Ivcf all_cohort_level.vcf --threads 10 --sample A --retain_work_dir --report_readid --genotype --min_size 50 --max_size 100000 --min_support 4 --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 > cutesv.log &
ls *.vcf > all_calls.txt
SURVIVOR merge all_calls.txt 1000 -1 1 -1 -1 -1 final_cohort.vcf

[Meltpinkg]

Hello, @lunky-zao

You can install the newest version from pip or GitHub and have another try.
By the way, does other types of SV still exist in the output VCF? In another word, only translocations in file all_cohort_level.vcf miss, the SV amount of other types keeps remaining?

Best,
Shuqi

[lunky-zao]

cuteSV's version is 2.0.3.
There is only translocations in file all_cohort_level.vcf miss.