2 hours ago by
Hi
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?
