Closed sachingadakh closed 1 month ago
Sorry, I think my previous answer was a bit misleading. It seems that your data is inappropriate for this approach. For reliable SV and SCNA calling, you need whole genome (not adaptive sampling) sequencing data at ideally ~20-30X (or higher) with matched normal sequencing data available too. Unfortunately, you seem to have shallow sequencing data, and no matched normal. Hope this makes sense! Carolin
Hello, Thank you for your suggestion on my previous issue #42. As per your suggestion in #42 , I ran the "savana cna" with the following command and received this error. Should I perform SV calling and phasing? However, I cannot because I do not have a normal sample, right? Besides, you had asked about the coverage and average read length in issue #42 . The coverage is around 1.23X by samtools depth and 1X by mosdepth. The average read size is 1.1 kb.
savana cna -t ../methyalation_data/dorado_meth_data/tumor.bam --outdir /disk2/ONT_files/ONT_methylation_analysis/CNV_data/savana/ --ref ../hg38.fa -w 1 Source: /home/rakieta/anaconda3/lib/python3.11/site-packages/savana/savana.py
... Allele counter will use threads = 24. (threads = 48 defined; threads = 24 available) ... Extracting phased heterozygous SNPs from None ... Traceback (most recent call last): File "/home/rakieta/anaconda3/bin/savana", line 10, in
sys.exit(main())
^^^^^^
File "/home/rakieta/anaconda3/lib/python3.11/site-packages/savana/savana.py", line 496, in main
args.func(args)
File "/home/rakieta/anaconda3/lib/python3.11/site-packages/savana/savana.py", line 193, in savana_cna
allele_counts_bed_path = allele_counter.perform_allele_counting(outdir, args.sample, args.phased_vcf, args.tumour, args.allele_mapq, args.allele_min_reads, args.threads)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rakieta/anaconda3/lib/python3.11/site-packages/savana/allele_counter.py", line 150, in perform_allele_counting
het_snps = extract_hets(phased_vcf)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rakieta/anaconda3/lib/python3.11/site-packages/savana/allele_counter.py", line 24, in extract_hets
vcf_reader = cyvcf2.VCF(phased_vcf)
^^^^^^^^^^^^^^^^^^^^^^
File "cyvcf2/cyvcf2.pyx", line 278, in cyvcf2.cyvcf2.VCF.init
File "cyvcf2/cyvcf2.pyx", line 205, in cyvcf2.cyvcf2.HTSFile._open_htsfile
OSError: Cannot open '<class 'NoneType'>' for writing.