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Old 11-11-2014, 05:59 PM   #5
yuelincoln
Junior Member
 
Location: hK

Join Date: Jun 2014
Posts: 5
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@westerman, thanks. Below is the results.
$ /usr/local/software/samtools-0.1.13/samtools view ./301-10.rmdup.bam | cut -f 3 | grep chr | uniq -c | more
3175288 chrM
568694 chr1
459726 chr2
351916 chr3
225789 chr4
493266 chr5
691892 chr6
348049 chr7
262928 chr8
138590 chr9
275147 chr10
209938 chr11
202256 chr12
150772 chr13
126969 chr14
193823 chr15
147602 chr16
167425 chr17
104782 chr18
73551 chr19
87570 chr20
43880 chr21
95365 chr22
529116 chrX
4396 chrY
28 chr1_gl000191_random

for hg19 is also right order.
$ head -10 /media/Analysis/gatk_resource/ucsc.hg19.fasta.fai
chrM 16571 6 50 51
chr1 249250621 16915 50 51
chr2 243199373 254252555 50 51
chr3 198022430 502315922 50 51
chr4 191154276 704298807 50 51
chr5 180915260 899276175 50 51
chr6 171115067 1083809747 50 51
chr7 159138663 1258347122 50 51
chr8 146364022 1420668565 50 51
chr9 141213431 1569959874 50 51
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