feat: add snpeff program to bin

bin/snpEff/LICENSE.md

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+
+Lincense: https://opensource.org/licenses/MIT
+
+Copyright 2021, Pablo Cingolani
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+

bin/snpEff/examples/cancer.ann.vcf

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+00:00:39.673	Reading cancer samples pedigree from file 'examples/samples_cancer_one.txt'.
+##SnpEffVersion="4.1 (build 2015-01-07), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -cancer -cancerSamples examples/samples_cancer_one.txt GRCh37.75 examples/cancer.vcf "
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient_01_Germline	Patient_01_Somatic
+1	69091	.	A	C,G	.	PASS	AC=1;ANN=G|start_lost|HIGH|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>G|p.Met1?|1/918|1/918|1/305||,G-C|start_lost|HIGH|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>G|p.Leu1?|1/918|1/918|1/305||WARNING_REF_DOES_NOT_MATCH_GENOME,C|initiator_codon_variant|LOW|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>C|p.Met1?|1/918|1/918|1/305||;LOF=(OR4F5|ENSG00000186092|1|1.00)	GT	1/0	2/1

bin/snpEff/examples/cancer.eff.vcf

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+##SnpEffVersion="4.1 (build 2015-01-07), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -classic -cancer -cancerSamples examples/samples_cancer_one.txt testHg3775Chr1 examples/cancer.vcf "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype_Number [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient_01_Germline	Patient_01_Somatic
+1	69091	.	A	C,G	.	PASS	AC=1;EFF=START_LOST(HIGH|MISSENSE|Atg/Gtg|M1V|305|OR4F5|protein_coding|CODING|ENST00000335137|1|G),START_LOST(HIGH|MISSENSE|Ctg/Gtg|L1V|305|OR4F5|protein_coding|CODING|ENST00000335137|1|G-C|WARNING_REF_DOES_NOT_MATCH_GENOME),NON_SYNONYMOUS_START(LOW|MISSENSE|Atg/Ctg|M1L|305|OR4F5|protein_coding|CODING|ENST00000335137|1|C);LOF=(OR4F5|ENSG00000186092|1|1.00)	GT	1/0	2/1

bin/snpEff/examples/cancer.vcf

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+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient_01_Germline	Patient_01_Somatic
+1	69091	.	A	C,G	.	PASS	AC=1	GT	1/0	2/1

bin/snpEff/examples/cancer_pedigree.ann.vcf

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+##PEDIGREE=<Derived=Patient_01_Somatic,Original=Patient_01_Germline>
+##SnpEffVersion="4.1 (build 2015-01-07), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -cancer testHg3775Chr1 examples/cancer_pedigree.vcf "
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient_01_Germline	Patient_01_Somatic
+1	69091	.	A	C,G	.	PASS	AF=0.1122;ANN=G|start_lost|HIGH|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>G|p.Met1?|1/918|1/918|1/305||,G-C|start_lost|HIGH|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>G|p.Leu1?|1/918|1/918|1/305||WARNING_REF_DOES_NOT_MATCH_GENOME,C|initiator_codon_variant|LOW|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>C|p.Met1?|1/918|1/918|1/305||;LOF=(OR4F5|ENSG00000186092|1|1.00)	GT	1/0	2/1
+1	69849	.	G	A,C	.	PASS	AF=0.1122;ANN=A|stop_gained|HIGH|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.759G>A|p.Trp253*|759/918|759/918|253/305||,C-A|stop_lost|HIGH|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.759G>C|p.Ter253Cysext*?|759/918|759/918|253/305||WARNING_REF_DOES_NOT_MATCH_GENOME,C|missense_variant|MODERATE|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.759G>C|p.Trp253Cys|759/918|759/918|253/305||	GT	1/0	2/1
+1	69511	.	A	C,G	.	PASS	AF=0.3580;ANN=C|missense_variant|MODERATE|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.421A>C|p.Thr141Pro|421/918|421/918|141/305||,G|missense_variant|MODERATE|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.421A>G|p.Thr141Ala|421/918|421/918|141/305||,G-C|missense_variant|MODERATE|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.421A>G|p.Pro141Ala|421/918|421/918|141/305||WARNING_REF_DOES_NOT_MATCH_GENOME	GT	1/1	2/2

bin/snpEff/examples/cancer_pedigree.vcf

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+##PEDIGREE=<Derived=Patient_01_Somatic,Original=Patient_01_Germline>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient_01_Germline	Patient_01_Somatic
+1	69091	.	A	C,G	.	PASS	AF=0.1122	GT	1/0	2/1
+1	69849	.	G	A,C	.	PASS	AF=0.1122	GT	1/0	2/1
+1	69511	.	A	C,G	.	PASS	AF=0.3580	GT	1/1	2/2

bin/snpEff/examples/example_motif.vcf

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+1	1060235	.	G	A	.	PASS	AC=16
+1	1250957	.	G	A	.	PASS	AC=9
+1	1310924	.	T	C	.	PASS	AC=948
+1	1368599	.	A	C	.	PASS	AC=920
+1	2182470	.	G	A	.	PASS	AC=743
+1	2466633	.	A	G	.	PASS	AC=770
+1	2480337	.	G	A	.	PASS	AC=16

bin/snpEff/examples/examples.sh

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+#!/bin/sh
+
+#-------------------------------------------------------------------------------
+#
+# Command lines for SnpEff's manua (examples)
+#
+#
+#                                                                Pablo Cingolani
+#-------------------------------------------------------------------------------
+
+genome="GRCh37.75"
+genome="testHg3775Chr1"			# Note: Sometimes we can use testHg3775Chr1 instead of GRCh37.75 ('testHg3775Chr1' only loads chr1 so it's faster)
+genome22="testHg3775Chr22"		# Note: Sometimes we can use testHg3775Chr22 instead of GRCh37.75 ('testHg3775Chr22' only loads chr22 so it's faster)
+
+#---
+# Multiple annotations per variant examples
+#---
+
+# java -Xmx4g -jar snpEff.jar $genome examples/variants_1.vcf > examples/variants_1.ann.vcf
+# 
+# java -Xmx4g -jar snpEff.jar $genome examples/variants_2.vcf > examples/variants_2.ann.vcf
+
+#---
+# Cancer examples
+#---
+
+# java -Xmx4g -jar snpEff.jar -v -cancer -cancerSamples examples/samples_cancer_one.txt $genome examples/cancer.vcf > examples/cancer.ann.vcf
+# 
+# java -Xmx4g -jar snpEff.jar -v -classic -cancer -cancerSamples examples/samples_cancer_one.txt $genome examples/cancer.vcf > examples/cancer.eff.vcf
+# 
+# java -Xmx4g -jar snpEff.jar -v -cancer $genome examples/cancer_pedigree.vcf > examples/cancer_pedigree.ann.vcf
+
+#---
+# Regulatory variants
+#---
+
+# java -Xmx4g -jar snpEff.jar -v -reg HeLa-S3 -reg NHEK $genome examples/test.1KG.vcf > examples/test.1KG.ann_reg.vcf
+
+#---
+# Encode example
+#---
+
+# # Create a directory for ENCODE files
+# mkdir -p db/encode
+# 
+# # Download ENCODE experimental results (BigBed file)
+# cd db/encode
+# wget "http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnase8988T.fdr01peaks.hg19.bb"
+# cd -
+#
+# # Annotate using ENCODE's data:
+# java -Xmx4g -jar snpEff.jar -v -interval db/encode/wgEncodeDukeDnase8988T.fdr01peaks.hg19.bb $genome examples/test.1KG.vcf > examples/test.1KG.ann_encode.vcf
+
+#---
+# Annotation example
+#---
+
+# java -Xmx4g -jar snpEff.jar -v $genome22 examples/test.chr22.vcf > examples/test.chr22.ann.vcf
+
+#---
+# SnpSift Filter examples
+#---
+
+#java -jar SnpSift.jar filter "ANN[0].EFFECT = 'missense_variant'" examples/test.chr22.ann.vcf > examples/test.chr22.ann.filter_missense_first.vcf
+
+#java -jar SnpSift.jar filter "ANN[*].EFFECT = 'missense_variant'" examples/test.chr22.ann.vcf > examples/test.chr22.ann.filter_missense_any.vcf
+
+#java -jar SnpSift.jar filter "(ANN[*].EFFECT = 'missense_variant') && (ANN[*].GENE = 'TRMT2A')" examples/test.chr22.ann.vcf > examples/test.chr22.ann.filter_missense_any_TRMT2A.vcf
+
+#java -jar SnpSift.jar filter "( GEN[HG00096].DS > 0.2 ) & ( GEN[HG00097].DS > 0.5 )" examples/1kg.head_chr1.vcf.gz > examples/1kg.head_chr1.filtered.vcf
+#gzip examples/1kg.head_chr1.filtered.vcf
+
+#---
+# SnpSift extractFields examples
+#---
+
+#java -jar SnpSift.jar extractFields -s "," -e "." examples/test.chr22.ann.vcf CHROM POS REF ALT "ANN[*].EFFECT" "ANN[*].HGVS_P" > examples/test.chr22.ann.txt
+
+#java -jar SnpSift.jar extractFields examples/test.chr22.ann.vcf CHROM POS REF ALT "ANN[*].EFFECT" > examples/test.chr22.ann.txt
+
+#cat examples/test.chr22.ann.vcf \
+#	| ./scripts/vcfEffOnePerLine.pl \
+#	| java -jar SnpSift.jar extractFields - CHROM POS REF ALT "ANN[*].EFFECT" \
+#	> examples/test.chr22.ann.one_per_line.txt
+
+# java -jar SnpSift.jar extractFields examples/1kg.head_chr1.vcf.gz CHROM POS REF ALT "GEN[HG00096].DS" "GEN[HG00097].DS" #> examples/1kg.head_chr1.txt

bin/snpEff/examples/intervals.bed

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+2L	10000	10999
+2L	12000	12999
+2L	14000	14999
+2L	16000	16999
+2L	18000	18999

bin/snpEff/examples/my_annotations.bed

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+1	10000	20000	MY_ANNOTATION

bin/snpEff/examples/samples_cancer.txt

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+Patient_01_Germline	Patient_01_Somatic
+Patient_02_Germline	Patient_02_Somatic
+Patient_03_Germline	Patient_03_Somatic
+Patient_04_Germline	Patient_04_Somatic

bin/snpEff/examples/samples_cancer_one.txt

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+Patient_01_Germline	Patient_01_Somatic