diff --git a/bin/parse_mixMHC2pred.py b/bin/parse_mixMHC2pred.py index 1e72c20..987439c 100755 --- a/bin/parse_mixMHC2pred.py +++ b/bin/parse_mixMHC2pred.py @@ -76,6 +76,8 @@ def parse_vcf(vep_vcf, sample_name, normal_name): enst = CSQ[6] variant = CSQ[14] + CSQ[15] + gene_symbol = gene_symbol if gene_symbol else ensg + vcf_record = { "chrom": chrom, "pos": pos, @@ -94,6 +96,7 @@ def parse_vcf(vep_vcf, sample_name, normal_name): "variant": variant, } + if "frameshift_variant" in variant_type.split("&"): key = gene_symbol + "_" + enst + "_" + CSQ[14] + ref + "/" + alt else: diff --git a/nextNEOpi.nf b/nextNEOpi.nf index b695b2a..8f476b0 100644 --- a/nextNEOpi.nf +++ b/nextNEOpi.nf @@ -5433,6 +5433,7 @@ if(!iedb_chck_file.exists() || iedb_chck_file.isEmpty()) { """ CWD=`pwd` cd /opt/iedb/ + rm -f $mhci_file wget $iedb_MHCI_url tar -xzvf $mhci_file cd mhc_i @@ -5440,6 +5441,7 @@ if(!iedb_chck_file.exists() || iedb_chck_file.isEmpty()) { cd /opt/iedb/ rm -f $mhci_file + rm -f $mhcii_file wget $iedb_MHCII_url tar -xzvf $mhcii_file cd mhc_ii