Alignments on IGV display not matched to the result from "samtools mpileup"
2
0
Entering edit mode
6 weeks ago
magicRG ▴ 30

I had two .bam files from the same reference genome sequences. When I used the command of "samtools mpileup " to find SNPs/InDels. The command is

samtools mpileup -r chr1:1204393-1204593 -q 1 -f /data/ucsc/hg38/hg38.fa ../003-picard/pt_01_WES_NORMAL.bam ../003-picard/pt_01_WES_TUMOR.bam

The result not was matched to what IVG displayed. For example: the pileup line

chr1    1204493 T   116 .$,$,,..,,,,,,,....,.,,,,,,.,,,,,,,,,.....,,,..,.........,..,.,,.,,..,..,,......,...,..,.,........,..,...,......,,,,,.  <AAAJFFFJJJJJJMFJJFJJJJJJJJJJJAJJJJFJJJJJJ7JAJ<<JAFFAJJFJJA>A7J<<FJ77J<A<FJ7FA<<JF<JJ<FFJAJF<JFJ<JJ7JJJ7JJJFFF<7A<<J    104 .,,,.,.,.,,.,,,,,,..,..,,,,.,...,,,..,,..,.,.,,,.,,........,,,..,..,,...g,....,,.......g,,,..g,,.g,g,,,,    <FFFJFF<JJJAJJJJJFJJFJFJJJJJJFJFJJJJJJJAJAJJJF<FA<JJFA7AAJF<7FFFFJJ<7FFJA7AJJJ<<FFFFJJJ7A77AAF<7J<77F7F6

As the pileup result, the sequences from "pt_01_WES_NORMAL.bam" should be all matched at this location, and the sequences from "pt_01_WES_TUMOR.bam" was only one SNP (T->G).

But the display of "pt_01_WES_NORMAL.bam" is

chr1:1,204,493
---------------------
Total count: 151
A : 0
C : 0
G : 15 (10%, 1+, 14- )
T : 136 (90%, 67+, 69- )
N : 0

and the display of "pt_01_WES_TUMOR.bam" is

chr1:1,204,493
 -------------------
 Total count: 126
 A : 0
 C : 1 (1%, 1+, 0- )
 G : 15 (12%, 1+, 14- )
 T : 110 (87%, 49+, 61- )
 N : 0

Display on IGV

What wrong about the discrepancy?

IGV Alignments mpileup • 242 views
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3
Entering edit mode
6 weeks ago
magicRG ▴ 30

I have found the problem. The default parameter ( "-Q") of "samtools mpileup" is 13. When setting it to 0, the result agreed with that IGV displayed.

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0
Entering edit mode
6 weeks ago
rob234king ▴ 610

IGV down samples by default, check settings in preferences you uncheck option then they should match up

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Thanks for you replay! Which option should be checked?

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