===== SNP与INDEL进行ANNOVAR注释  =====
====说明====
项目中我们为老师提供了SNP和INDEL的信息，但没有提供snp在基因功能域上的分布以及是否引起同义非同义突变等信息（新版本转录流程已增加snpeff注释）。客户往往要求增加ANNOVAR注释，此脚本可实现该功能。

===主要结果：===
**SNPs.avinput.invalid_input(功能域注释)**

**SNPS.avinput.exonic_variant_function（同义非同义突变注释)**

**INDEL.avinput.variant_function(功能域注释)**

**README.txt**
====脚本位置====

/TJPROJ6/RNA_SH/TJPROJ1/RNA/shouhou/script_dir/script_dir/ref/ANNOVAR/annovar_annotation.pl


<code>
Options
        -dir <s> :result folder of SNPs and INDEL
        -gtf <i>: gtf file
        -fa <s>: genome fa file
	-vcf <s>: yes or not
        -outdir <s>: pathway of outdir
        -h|?|help : Show this help
</code>
====运行示例====
<code>
perl /TJPROJ1/RNA/shouhou/script_dir/ref/ANNOVAR/annovar_annotation.pl \ 
  -dir /BJPROJ/RNA/shouhou/NHT160504/20171201_snp/SNP/ResultsQ30/SNP \
  -outdir /BJPROJ/RNA/shouhou/NHT160504/20171201_snp/SNP/ResultsQ30/SNP_ANNOVAR \
  -fa /BJPROJ/RNA/reference_data/Animal/Homo_sapiens/refenerce_hg19/hg19.fa \
  -gtf /BJPROJ/RNA/reference_data/Animal/Homo_sapiens/refenerce_hg19/ncRNA/Homo_sapiens.GRCh37.82.chr_rename.gtf \
  -vcf no \

</code>


====结果展示====
===avinput.invalid_input(功能域注释)===
<code>
intergenic      NONE(dist=NONE),ENSG00000251841(dist=2656)      chrY    2650134 2650134 C       G       NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      0,2     NA      NA
upstream        ENSG00000251841 chrY    2652068 2652068 A       G       NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA
upstream        ENSG00000251841 chrY    2652093 2652093 A       G       NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA
downstream      ENSG00000251841 chrY    2653141 2653141 T       C       NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      0,5
downstream      ENSG00000251841 chrY    2653395 2653395 A       G       NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA
exonic  ENSG00000184895 chrY    2655180 2655180 G       A       NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA
</code>
===avinput.exonic_variant_function（同义非同义突变注释)===
<code>
line6   synonymous SNV  ENSG00000184895:ENST00000383070:exon1:c.C465T:p.S155S,ENSG00000184895:ENST00000525526:exon1:c.C465T:p.S155S,ENSG00000184895:ENST00000534739:exon1:c.C465T:p.S155S,      chrY    265
line7   synonymous SNV  ENSG00000184895:ENST00000383070:exon1:c.C216T:p.R72R,ENSG00000184895:ENST00000525526:exon1:c.C216T:p.R72R,ENSG00000184895:ENST00000534739:exon1:c.C216T:p.R72R, chrY    2655429 265
line135 synonymous SNV  ENSG00000129824:ENST00000430575:exon7:c.C738T:p.S246S,ENSG00000129824:ENST00000250784:exon7:c.C711T:p.S237S,    chrY    2734854 2734854 C       T       NA      NA      NA      NA
line830 nonsynonymous SNV       ENSG00000099715:ENST00000215473:exon1:c.G343C:p.E115Q,ENSG00000099715:ENST00000333703:exon4:c.G310C:p.E104Q,ENSG00000099715:ENST00000362095:exon1:c.G343C:p.E115Q,      chr
line832 nonsynonymous SNV       ENSG00000099715:ENST00000215473:exon2:c.G2749T:p.V917F,ENSG00000099715:ENST00000333703:exon5:c.G2716T:p.V906F,ENSG00000099715:ENST00000362095:exon2:c.G2749T:p.V917F,   chr
line833 nonsynonymous SNV       ENSG00000099715:ENST00000215473:exon2:c.T3036G:p.N1012K,ENSG00000099715:ENST00000333703:exon5:c.T3003G:p.N1001K,ENSG00000099715:ENST00000362095:exon2:c.T3036G:p.N1012K,
line1133        synonymous SNV  ENSG00000092377:ENST00000355162:exon7:c.T402C:p.P134P,ENSG00000092377:ENST00000346432:exon7:c.T402C:p.P134P,ENSG00000092377:ENST00000383032:exon8:c.T402C:p.P134P,      chr
line1134        nonsynonymous SNV       ENSG00000092377:ENST00000355162:exon7:c.G442A:p.G148R,ENSG00000092377:ENST00000346432:exon7:c.G442A:p.G148R,ENSG00000092377:ENST00000383032:exon8:c.G442A:p.G148R,
line1154        nonsynonymous SNV       ENSG00000092377:ENST00000355162:exon16:c.G1282A:p.A428T,ENSG00000092377:ENST00000346432:exon16:c.G1282A:p.A428T,ENSG00000092377:ENST00000383032:exon17:c.G1282A:p.A
line3428        nonsynonymous SNV       ENSG00000114374:ENST00000338981:exon4:c.G195T:p.E65D,   chrY    14832620        14832620        G       T       NA      NA      NA      NA      NA      NA      NA
line3462        nonsynonymous SNV       ENSG00000114374:ENST00000338981:exon12:c.C1385G:p.S462C,        chrY    14851526        14851526        C       G       NA      NA      NA      NA      NA      NA
line3487        nonsynonymous SNV       ENSG00000114374:ENST00000338981:exon13:c.G1594A:p.A532T,        chrY    14869293        14869293        G       A       NA      NA      NA      NA      NA      NA
line3518        nonsynonymous SNV       ENSG00000114374:ENST00000338981:exon23:c.G3178A:p.A1060T,       chrY    14898163        14898163        G       A       NA      NA      NA      NA      NA      NA
</code>