From bfde8cd27bbae5d3e9b6a02d453e2fb781243031 Mon Sep 17 00:00:00 2001 From: Matteo Barcella Date: Fri, 4 Aug 2023 10:31:48 +0000 Subject: [PATCH] Update README.md --- WES/README.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/WES/README.md b/WES/README.md index adea06a..d4413ad 100644 --- a/WES/README.md +++ b/WES/README.md @@ -74,7 +74,13 @@ SnpSift dbnsfp -db dbNSFP4.0a/dbNSFP4.0a.txt.gz -v ${sampleid}\_dbsnp_cc_cnc_ref We leverage SnpSift extractfield function for selecting fields of interest and performing Allele Fraction analysis. -`SnpSift extractFields ${sampleid}_dbsnp_cc_cnc_dbnsfp_refseq_light_filtered.vcf CHROM POS REF ALT GEN[0].AF GEN[0].DP GEN[0].AD[0] GEN[0].AD[1] GEN[0].GT ID FILTER ANN[0].HGVS_P ANN[0].GENE ANN[0].BIOTYPE ANN[0].RANK ANN[0].EFFECT ANN[0].IMPACT COMMON G5 dbNSFP_ExAC_Adj_AF dbNSFP_1000Gp3_AF dbNSFP_ExAC_AF dbNSFP_phastCons100way_vertebrate dbNSFP_FATHMM_pred dbNSFP_GERP___RS dbNSFP_GERP___NR dbNSFP_CADD_phred dbNSFP_MetaSVM_pred dbNSFP_LRT_pred dbNSFP_PROVEAN_pred dbNSFP_MutationTaster_pred dbNSFP_MutationAssessor_pred dbNSFP_SIFT_pred dbNSFP_Polyphen2_HVAR_pred dbNSFP_Polyphen2_HDIV_pred > ${sampleid}_dbsnp_cc_cnc_dbnsfp_refseq_light_raw_filtered.fields.txt` +``` +- SnpSift extractFields ${sampleid}_dbsnp_cc_cnc_dbnsfp_refseq_light_filtered.vcf CHROM POS REF ALT GEN[0].AF GEN[0].DP GEN[0].AD[0] GEN[0].AD[1] GEN[0].GT ID FILTER ANN[0].HGVS_P ANN[0].GENE ANN[0].BIOTYPE ANN[0].RANK ANN[0].EFFECT ANN[0].IMPACT COMMON G5 dbNSFP_ExAC_Adj_AF dbNSFP_1000Gp3_AF dbNSFP_ExAC_AF dbNSFP_phastCons100way_vertebrate dbNSFP_FATHMM_pred dbNSFP_GERP___RS dbNSFP_GERP___NR dbNSFP_CADD_phred dbNSFP_MetaSVM_pred dbNSFP_LRT_pred dbNSFP_PROVEAN_pred dbNSFP_MutationTaster_pred dbNSFP_MutationAssessor_pred dbNSFP_SIFT_pred dbNSFP_Polyphen2_HVAR_pred dbNSFP_Polyphen2_HDIV_pred > ${sampleid}_dbsnp_cc_cnc_dbnsfp_refseq_light_raw_filtered.fields.txt +- SnpSift extractFields ${sampleid}_dbsnp_cc_cnc_dbnsfp_refseq_light_raw.vcf CHROM POS REF ALT GEN[0].AF GEN[0].DP GEN[0].AD[0] GEN[0].AD[1] GEN[0].GT ID FILTER ANN[0].HGVS_P ANN[0].GENE ANN[0].BIOTYPE ANN[0].RANK ANN[0].EFFECT ANN[0].IMPACT COMMON G5 dbNSFP_ExAC_Adj_AF dbNSFP_1000Gp3_AF dbNSFP_ExAC_AF dbNSFP_phastCons100way_vertebrate dbNSFP_FATHMM_pred dbNSFP_GERP___RS dbNSFP_GERP___NR dbNSFP_CADD_phred dbNSFP_MetaSVM_pred dbNSFP_LRT_pred dbNSFP_PROVEAN_pred dbNSFP_MutationTaster_pred dbNSFP_MutationAssessor_pred dbNSFP_SIFT_pred dbNSFP_Polyphen2_HVAR_pred dbNSFP_Polyphen2_HDIV_pred > ${sampleid}_dbsnp_cc_cnc_dbnsfp_refseq_light_raw.fields.txt +``` + + + -- GitLab