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2 hours ago by


I have a big annovar annotation of my SNV and INDEL from whole genome sequencing

In chromosome column I have chr 1 to 22 and another contigs like

> unique(anno_maf$Chromosome)
 [1] "chr1"                  "chr6"                 
 [3] "chr16"                 "chr17"                
 [5] "chr20"                 "chr2"                 
 [7] "chr3"                  "chr4"                 
 [9] "chr14"                 "chr19"                
[11] "chr5"                  "chr10"                
[13] "chr9"                  "chr12"                
[15] "chr13"                 "chr11"                
[17] "chr22"                 "chr7"                 
[19] "chr15"                 "chr8"                 
[21] "chr18"                 "chr21"                
[23] "chrX"                  "chrY"                 
[25] "chr4_gl000194_random"  "chr17_gl000205_random"
[27] "chrUn_gl000241"        "hs37d5"               
[29] "chrUn_gl000219"        "chrUn_gl000234"       
[31] "chr1_gl000191_random"  "chrUn_gl000211"       
[33] "chrUn_gl000224"        "chrUn_gl000225"       
[35] "chr17_gl000203_random" "chrUn_gl000212"       
[37] "chrUn_gl000243"        "chrUn_gl000214"       
[39] "chrM"                  "chr1_gl000192_random" 
[41] "chr7_gl000195_random"  "chrUn_gl000232"       
[43] "chr4_gl000193_random"  "chr19_gl000208_random"
[45] "chrUn_gl000226"        "chrUn_gl000218"       
[47] "chr9_gl000199_random"  "chrUn_gl000217"       
[49] "chrUn_gl000229"        "chrUn_gl000216"       
[51] "chrUn_gl000231"        "chr9_gl000198_random" 
[53] "chr17_gl000204_random" "chrUn_gl000220"       
[55] "chrUn_gl000235"        "chr11_gl000202_random"
[57] "chrUn_gl000222"        "chrUn_gl000240"       
[59] "chrUn_gl000233"        "chrUn_gl000230"       
[61] "chrUn_gl000213"        "chrUn_gl000238"       
[63] "chr19_gl000209_random" "chrUn_gl000237"       
[65] "#CHROM"

In your experiences, should I ignore anything else than chromosome 1 to chromosome 21 in my analysis? I mean for instance if my goal is comparing some somatic variations and copy number changes in two different conditions, does it make sense to analysis only chr 1 to 21 ignoring the rest of random or non well annotated parts of genome? Does it hurt at all?


2 hours ago


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