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Commit aba1e70e authored by Matteo Barcella's avatar Matteo Barcella
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Update README.md

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...@@ -43,26 +43,35 @@ Below the workflow and commands used: ...@@ -43,26 +43,35 @@ Below the workflow and commands used:
We implemented several layers of annotation using different datasets including [SNPeff](http://pcingola.github.io/SnpEff/) (v.86), [dbSNP](https://www.ncbi.nlm.nih.gov/snp/) (v.152), [dbNSFP4](http://database.liulab.science/dbNSFP) (4.0a for academic). We implemented several layers of annotation using different datasets including [SNPeff](http://pcingola.github.io/SnpEff/) (v.86), [dbSNP](https://www.ncbi.nlm.nih.gov/snp/) (v.152), [dbNSFP4](http://database.liulab.science/dbNSFP) (4.0a for academic).
``` ```
snpEff -v -csvStats ${sampleid}\_rawstats_canon.csv -s ${sampleid}\_rawstats_canon.html -canon GRCh38.86 Mutect2_raw_call_${sampleid}\_exome_refseq_light_filtered.vcf.gz > $sampleid\_raw_annot_refseq_light_filtered.vcf snpEff -v -csvStats SampleID_rawstats_canon.csv -s SampleID_rawstats_canon.html -canon GRCh38.86 Mutect2_raw_call_SampleID_exome_refseq_light_filtered.vcf.gz > SampleID_raw_annot_refseq_light_filtered.vcf
# dbSNP annotation # dbSNP annotation
SnpSift annotate $dbsnp ${sampleid}\_raw_annot_refseq_light_filtered.vcf > ${sampleid}\_dbsnp_refseq_light_filtered.vcf SnpSift annotate $dbsnp SampleID_raw_annot_refseq_light_filtered.vcf > SampleID_dbsnp_refseq_light_filtered.vcf
gatk IndexFeatureFile -I ${sampleid}\_dbsnp_refseq_light_filtered.vcf gatk IndexFeatureFile -I SampleID_dbsnp_refseq_light_filtered.vcf
# Cosmic annotation (coding) # Cosmic annotation (coding)
SnpSift annotate $cosmic ${sampleid}\_dbsnp_refseq_light_filtered.vcf > ${sampleid}\_dbsnp_cc_refseq_light_filtered.vcf SnpSift annotate $cosmic SampleID_dbsnp_refseq_light_filtered.vcf > SampleID_dbsnp_cc_refseq_light_filtered.vcf
gatk IndexFeatureFile -I ${sampleid}\_dbsnp_cc_refseq_light_filtered.vcf gatk IndexFeatureFile -I SampleID_dbsnp_cc_refseq_light_filtered.vcf
# Cosmic annotation (non coding) # Cosmic annotation (non coding)
SnpSift annotate $cosmicnc ${sampleid}\_dbsnp_cc_refseq_light_filtered.vcf > ${sampleid}\_dbsnp_cc_cnc_refseq_light_filtered.vcf SnpSift annotate $cosmicnc SampleID_dbsnp_cc_refseq_light_filtered.vcf > SampleID_dbsnp_cc_cnc_refseq_light_filtered.vcf
gatk IndexFeatureFile -I ${sampleid}\_dbsnp_cc_cnc_refseq_light_filtered.vcf gatk IndexFeatureFile -I SampleID_dbsnp_cc_cnc_refseq_light_filtered.vcf
# dbNSFP4 annotation # dbNSFP4 annotation
SnpSift dbnsfp -db dbNSFP4.0a/dbNSFP4.0a.txt.gz -v ${sampleid}\_dbsnp_cc_cnc_refseq_light_filtered.vcf > ${sampleid}\_dbsnp_cc_cnc_dbnsfp_refseq_light_filtered.vcf SnpSift dbnsfp -db dbNSFP4.0a/dbNSFP4.0a.txt.gz -v SampleID_dbsnp_cc_cnc_refseq_light_filtered.vcf > SampleID_dbsnp_cc_cnc_dbnsfp_refseq_light_filtered.vcf
# NOTE: a pass-only version is also produced by picking-up only PASS variants:
bcftools_viewCommand=view -f PASS -O z Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10.vcf.gz
- SnpEff -csvStats SampleID_rawstats_canon.csv -s SampleID_rawstats_canon.html GRCh38.86 Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10_PASS.vcf.gz
- SnpSift Annotate dbSNP.v152.vcf.gz SampleID_raw_annot_refseq_light.vcf
- SnpSift Annotate CosmicCodingMuts.vcf.gz SampleID_dbsnp_refseq_light.vcf
- SnpSift Annotate CosmicNonCodingVariants.vcf.gz SampleID_dbsnp_cc_refseq_light.vcf
- SnpSift DbNsfp SampleID_dbsnp_cc_cnc_refseq_light.vcf
``` ```
...@@ -71,7 +80,10 @@ SnpSift dbnsfp -db dbNSFP4.0a/dbNSFP4.0a.txt.gz -v ${sampleid}\_dbsnp_cc_cnc_ref ...@@ -71,7 +80,10 @@ 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.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.fields.txt
``` ```
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