making reference from ucsc : include or not - chrUn

[dkrtndhkd]

Hi, I have simple question.

i'm using hg19 reference from ucsc.

i downloaded 93 chr*.fa file (1~23, X, Y, MT, Un_*, gl*);
chr1.fa
chr10.fa
chr11.fa
chr11_gl000202_random.fa
chr12.fa
chr13.fa
chr14.fa
chr15.fa
chr16.fa
chr17.fa
chr17_ctg5_hap1.fa
chr17_gl000203_random.fa
chr17_gl000204_random.fa
chr17_gl000205_random.fa
chr17_gl000206_random.fa
chr18.fa
chr18_gl000207_random.fa
chr19.fa
chr19_gl000208_random.fa
chr19_gl000209_random.fa
chr1_gl000191_random.fa
chr1_gl000192_random.fa
chr2.fa
chr20.fa
chr21.fa
chr21_gl000210_random.fa
chr22.fa
chr3.fa
chr4.fa
chr4_ctg9_hap1.fa
chr4_gl000193_random.fa
chr4_gl000194_random.fa
chr5.fa
chr6.fa
chr6_apd_hap1.fa
chr6_cox_hap2.fa
chr6_dbb_hap3.fa
chr6_mann_hap4.fa
chr6_mcf_hap5.fa
chr6_qbl_hap6.fa
chr6_ssto_hap7.fa
chr7.fa
chr7_gl000195_random.fa
chr8.fa
chr8_gl000196_random.fa
chr8_gl000197_random.fa
chr9.fa
chr9_gl000198_random.fa
chr9_gl000199_random.fa
chr9_gl000200_random.fa
chr9_gl000201_random.fa
chrM.fa
chrUn_gl000211.fa
chrUn_gl000212.fa
chrUn_gl000213.fa
chrUn_gl000214.fa
chrUn_gl000215.fa
chrUn_gl000216.fa
chrUn_gl000217.fa
chrUn_gl000218.fa
chrUn_gl000219.fa
chrUn_gl000220.fa
chrUn_gl000221.fa
chrUn_gl000222.fa
chrUn_gl000223.fa
chrUn_gl000224.fa
chrUn_gl000225.fa
chrUn_gl000226.fa
chrUn_gl000227.fa
chrUn_gl000228.fa
chrUn_gl000229.fa
chrUn_gl000230.fa
chrUn_gl000231.fa
chrUn_gl000232.fa
chrUn_gl000233.fa
chrUn_gl000234.fa
chrUn_gl000235.fa
chrUn_gl000236.fa
chrUn_gl000237.fa
chrUn_gl000238.fa
chrUn_gl000239.fa
chrUn_gl000240.fa
chrUn_gl000241.fa
chrUn_gl000242.fa
chrUn_gl000243.fa
chrUn_gl000244.fa
chrUn_gl000245.fa
chrUn_gl000246.fa
chrUn_gl000247.fa
chrUn_gl000248.fa
chrUn_gl000249.fa
chrX.fa
chrY.fa


when using GATK, i have some problem because of reference contigs.

do i need to cat all these files? or just 1~23, X, Y, MT?

and somebody please tell me what's the meaning of weird(for me) file name like gl, hap1~7, random?

[yumtaoist]

The ChrUn should be included. Although it can not be located to the chromsome, it is part of the genome. Many reads are coming from it.