and got the following error:
Traceback (most recent call last):
File "/usr/bin/CrossMap.py", line 1932, in
crossmap_vcf_file(mapping = mapTree, infile= in_file, outfile = out_file, liftoverfile = sys.argv[2], refgenome = genome_file)
File "/usr/bin/CrossMap.py", line 608, in crossmap_vcf_file
fields[4] = revcomp_DNA(fields[4], True)
File "/usr/bin/CrossMap.py", line 106, in revcomp_DNA
return ''.join([complement[base] for base in reversed(seq)])
File "/usr/bin/CrossMap.py", line 106, in
return ''.join([complement[base] for base in reversed(seq)])
KeyError: '-'
brianpenghe
commented
4 years ago
Hi, Used following command to liftover vcf file from GRCh37 to 38.
CrossMap.py vcf ~/bioinfo_tools/vcf-liftover/GRCh37_to_GRCh38.chain.gz final.combined_cancer_tcga.fixed.vcf.gz Homo_sapiens.GRCh38.dna.primary_assembly.fa hg38.final.combined_cancer_tcga.fixed.vcf
and got the following error: Traceback (most recent call last): File "/usr/bin/CrossMap.py", line 1932, in
crossmap_vcf_file(mapping = mapTree, infile= in_file, outfile = out_file, liftoverfile = sys.argv[2], refgenome = genome_file)
File "/usr/bin/CrossMap.py", line 608, in crossmap_vcf_file
fields[4] = revcomp_DNA(fields[4], True)
File "/usr/bin/CrossMap.py", line 106, in revcomp_DNA
return ''.join([complement[base] for base in reversed(seq)])
File "/usr/bin/CrossMap.py", line 106, in
return ''.join([complement[base] for base in reversed(seq)])
KeyError: '-'
Can you please help. Thanks