Dog_variant_calling

The analysis is to find nonsynonymous SNPs in coding regions that are unique in experiment groups by using RNA-seq data.

Name		Name	Last commit message	Last commit date
Latest commit History 31 Commits
1_Sample information		1_Sample information
2_Sample process		2_Sample process
3_STAR 2-pass mapping		3_STAR 2-pass mapping
4_Picard to create index		4_Picard to create index
5_GATK to variant calling		5_GATK to variant calling
6_Vcftools to filter DP and compare files		6_Vcftools to filter DP and compare files
7_VEP to annotate vcf file		7_VEP to annotate vcf file
8_filter SNVs that may alter the function of proteins		8_filter SNVs that may alter the function of proteins
Classification of coding SNVs (1).tif		Classification of coding SNVs (1).tif
Coutput1_filtered.vcf.recode.vcf.gz		Coutput1_filtered.vcf.recode.vcf.gz
Eoutput1_filtered.vcf.recode.vcf.gz		Eoutput1_filtered.vcf.recode.vcf.gz
Only_D.vcf.tar.gz		Only_D.vcf.tar.gz
Only_D_annotated.txt.zip		Only_D_annotated.txt.zip
Only_D_annotated.vcf.zip		Only_D_annotated.vcf.zip
README.md		README.md
VEP1.PNG		VEP1.PNG
VEP_2.PNG		VEP_2.PNG
frameshift_variant.txt		frameshift_variant.txt
inframe_deletion.txt		inframe_deletion.txt
inframe_insertion.txt		inframe_insertion.txt
missense_variant.txt		missense_variant.txt
nonsynonmous_R.xlsx		nonsynonmous_R.xlsx
tabix-0.2.6.zip		tabix-0.2.6.zip
vcftools-vcftools-ea875e2.zip		vcftools-vcftools-ea875e2.zip

XueMaryYu/Dog_variant_calling