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Commit bfde8cd2 authored by Matteo Barcella's avatar Matteo Barcella
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Update README.md

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...@@ -74,7 +74,13 @@ SnpSift dbnsfp -db dbNSFP4.0a/dbNSFP4.0a.txt.gz -v ${sampleid}\_dbsnp_cc_cnc_ref ...@@ -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. 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
```
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