truvari指标

[Bigdata20688]

你好，我在使用HG00733.svision.s5.graph.vcf.gz结果文件和pav_HG00733_CLR_SS_FLYE_PA.vcf.gz基准文件使用Truvari进行基准测试查看准确率和召回率出现Traceback (most recent call last):
File "/opt/conda/bin/truvari", line 8, in
sys.exit(main())
File "/opt/conda/lib/python3.9/site-packages/truvari/main.py", line 105, in main
TOOLSargs.cmd
File "/opt/conda/lib/python3.9/site-packages/truvari/bench.py", line 766, in bench_main
output = m_bench.run()
File "/opt/conda/lib/python3.9/site-packages/truvari/bench.py", line 495, in run
for match in itertools.chain.from_iterable(map(self.compare_chunk, chunks)):
File "/opt/conda/lib/python3.9/site-packages/truvari/matching.py", line 327, in chunker
if not matcher.filter_call(entry, key == 'base'):
File "/opt/conda/lib/python3.9/site-packages/truvari/matching.py", line 164, in filter_call
size = truvari.entry_size(entry)
File "/opt/conda/lib/python3.9/site-packages/truvari/comparisons.py", line 362, in entry_size
size = abs(entry.info["SVLEN"][0])
TypeError: bad operand type for abs(): 'str'

[jiadong324]

You might want to change the header of the PAV VCF header. The SVLEN in the info header should be somthing like this ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">.

Hope this help!

[Bigdata20688]

感谢您提供的帮助，但是按照您的操作，我尝试在pav_HG00733_CLR_SS_FLYE_PA.vcf文件开头加入您给的头部信息后，运行truvari bench -b /root/SVision/copmpare/pav_HG00733_CLR_SS_FLYE_PA.vcf.gz -c /root/SVision/home/user/svision_out/HG00733.svision.s5.graph.vcf.gz -o output_dir/该命令后，提示
Traceback (most recent call last):
File "/opt/conda/bin/truvari", line 8, in
sys.exit(main())
File "/opt/conda/lib/python3.9/site-packages/truvari/main.py", line 105, in main
TOOLSargs.cmd
File "/opt/conda/lib/python3.9/site-packages/truvari/bench.py", line 751, in bench_main
if check_params(args) or check_inputs(args):
File "/opt/conda/lib/python3.9/site-packages/truvari/bench.py", line 177, in check_inputs
b_check, args.bSample = check_sample(args.base, args.bSample)
File "/opt/conda/lib/python3.9/site-packages/truvari/bench.py", line 159, in check_sample
vcf_file = pysam.VariantFile(vcf_fn)
File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.init
File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file b'/root/SVision/copmpare/pav_HG00733_CLR_SS_FLYE_PA.vcf.gz' (mode=b'r') - is it VCF/BCF format?错误，有没有解决办法呢？

[Bigdata20688]

You might want to change the header of the PAV VCF header. The SVLEN in the info header should be somthing like this ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">.

Hope this help!

感谢您提供的帮助，但目前采用您的建议后遇到了问题，您可以再帮忙看一下吗？

[Bigdata20688]

或者您可以告诉一下我您的结果对比指标（准确率、召回率）是采用了什么方法吗？

[jiadong324]

We also use truvari bench in the paper, but it was a very old version of truvari (like v3.*)

Looks like it is the truvari issue, which version did you use? Please also check and confirm whether pav_HG00733_CLR_SS_FLYE_PA.vcf.gz is a valid VCF format or not. You can simply use bcftools view.