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songbowang125 / SVision-pro

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How to use SVision-pro to call SVs for assembly results #15

Open xuxingyubio opened 6 days ago

xuxingyubio commented 6 days ago

I have assembled a single haplotype and aligned it to the hg38 reference genome. Then, I used SVision to call structural variants (SVs). When I called SVs using each haplotype separately, both haplotypes returned a 1/1 genotype. However, when I merged the alignment results of the two haplotypes and ran SVision again, the output included both 1/1 and 1/0 genotypes.

I observed that some SVs appeared in the results of one haplotype but not in the other when calling SVs individually, yet the final merged result still reported a 1/1 genotype for these cases.

SVision-pro --preset asm --target_path ${sample}.bam --genome_path GCA_000001405.15_GRCh38_no_alt_analysis_set.fna --out_path /home/users/xyxu//SV --sample_name ${sample} --detect_mode germline --model_path /home/users/xyxu/SV/SVision-pro/src/pre_process/model_liteunet_256_8_16_32_32_32.pth --process_num 20 --min_supp 1

songbowang125 commented 4 days ago

We recommand that merging the two haplotyple BAM files together (samtools merge should work) and then using SVision-pro to call SVs.

If you input one haplotype BAM file once, the GT flag would always be 1/1 due to SVision-pro doesn't support phased assembly calling since it doesn't how many haplotypes in total. We will improve this in the next version for better supporting assembly-based SV calling.

Thanks.