snvcov in haplotype genome

[yeeus]

Hello Mr.Ruan,
I'm new to bioinformatics and genome assembly. I noticed SNV-Cov plot might be used for the redundancy in diploid genome. But, if I map the hifi reads of the child to the haplotype assembly assembled by hifiasm, is gaep useful to call snvs and can demonstrate the heterozygosity of the specific regions between parents?

[zy-optimistic]

Gaep can only use NGS reads to call SNVs with bcftools. If you only have HiFi reads, you can call SNVs using another tool for TGS SNV calling and then use the VCF file as input for 'gaep snvcov'.
Additionally, SNV-Cov plot cannot demonstrate the heterozygosity of specific regions, it reflcts the overall redundancy of genome assembly.

[yeeus]

I got some errors but the program didn't terminate...
Here is the log flie:

Error occurred while processing the filter "%QUAL<10 || DP <= 3" (1:1)
Thread 2 terminated abnormally: [var_calling] Can't run "path/bcftools filter  -e '%QUAL<10 || DP <= 3' gaep_cov_snp_dot_38489/variants/snv_depth_38489.h2tg000002l.vcf -o gaep_cov_snp_dot_38489/variants/snv_depth_38489.h2tg000002l.flt.vcf".
Error occurred while processing the filter "%QUAL<10 || DP <= 3" (1:1)
Thread 3 terminated abnormally: [var_calling] Can't run "path/bcftools filter  -e '%QUAL<10 || DP <= 3' gaep_cov_snp_dot_38489/variants/snv_depth_38489.h2tg000003l.vcf -o gaep_cov_snp_dot_38489/variants/snv_depth_38489.h2tg000003l.flt.vcf".
Error occurred while processing the filter "%QUAL<10 || DP <= 3" (1:1)
Thread 4 terminated abnormally: [var_calling] Can't run "path/bcftools filter  -e '%QUAL<10 || DP <= 3' gaep_cov_snp_dot_38489/variants/snv_depth_38489.h2tg000004l.vcf -o gaep_cov_snp_dot_38489/variants/snv_depth_38489.h2tg000004l.flt.vcf".
Error occurred while processing the filter "%QUAL<10 || DP <= 3" (1:1)
Thread 1 terminated abnormally: [var_calling] Can't run "path/bcftools filter  -e '%QUAL<10 || DP <= 3' gaep_cov_snp_dot_38489/variants/snv_depth_38489.h2tg000001l.vcf -o gaep_cov_snp_dot_38489/variants/snv_depth_38489.h2tg000001l.flt.vcf".

And here is my code:

gaep snvcov -r CN1_70x.dip.mat.p_ctg.fasta \
            -i mat/FF11_80x_R1.fq.gz \
            -I mat/FF11_80x_R2.fq.gz \
            -t 50 -f pdf -o mat -d mat_gaep

Best wishes!

[zy-optimistic]

I apologize for my delayed reply.Please try executing the relevant 'vcftools' command directly and check for any errors. If no errors occur, please run GAEP again.