Question: only chrM in the varscan2 copynumber output
0
gravatar for lhaiyan3
2.3 years ago by
lhaiyan330
United States
lhaiyan330 wrote:

Hi,

I want to use the varscan2 copynumber, but my output file just has the chrM, no other chr. I use the samtools idxstats to check my bam file. The bam file has all the chr, but chrM is the first. It looks like the program stops, but i did not get wrong message.

Here is my command line:

samtools mpileup   -q 1 -f $ref normal.bam tumor.bam| java -Xmx64g -jar $VARSCANHOME/varscan.jar copynumber varScan --mpileup 1

The tail of my output.copynumber file is,

chrM    15101   15200   100     254.0   134.8   -0.914  47.0
chrM    15201   15300   100     300.7   139.1   -1.112  47.0
chrM    15301   15400   100     262.9   127.0   -1.050  48.0
chrM    15401   15500   100     247.1   121.4   -1.025  47.0
chrM    15501   15600   100     228.7   118.0   -0.955  50.0
chrM    15601   15700   100     191.6   91.1    -1.073  41.0
chrM    15701   15800   100     168.0   65.3    -1.363  47.0
chrM    15801   15900   100     123.6   44.9    -1.459  37.0
chrM    15901   16000   100     109.3   53.2    -1.039  38.0
chrM    16001   16100   100     126.4   67.7    -0.901  40.0

Here is my running message,

[-] Unloading samtools 1.3.1 ...
[+] Loading samtools 1.2 ...

The following have been reloaded with a version change:
  1) samtools/1.3.1 => samtools/1.2

[+] Loading varscan 2.4.2 ...
[mpileup] 2 samples in 2 input files
<mpileup> Set max per-file depth to 4000
Min coverage:   10
Min avg qual:   15
P-value thresh: 0.01
Reading input from STDIN
Reading mpileup input...
Parsing Exception on line:
chrM    16184   C       0                       0
8

Can anyone please give me some suggestions? Thanks very much for the help.

best

HY

chrm varscan2 copynumber • 824 views
ADD COMMENTlink modified 2.3 years ago by WouterDeCoster38k • written 2.3 years ago by lhaiyan330

Duplicate of ChrM in the Varscan2 copynumber output

Parsing Exception on line: chrM    16184   C       0   0  8

That's an error message

Using google brought up: https://sourceforge.net/p/varscan/discussion/1073559/thread/f710f748/ and http://seqanswers.com/forums/showthread.php?t=26699

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by WouterDeCoster38k

Thanks for the information. I found this post, Problem generating Varscn2 copynumber output, and then change my command to :

samtools mpileup -q 1 -f ref.fasta n.bam t.bam |\ awk -F"\t" '$4 > 0 && $7 > 0' |\ java -jar VarScan.v2.3.7.jar copynumber out.bn --mpileup 1

I can get other chr copy number change.

ADD REPLYlink written 2.3 years ago by lhaiyan330

Good, next time first try searching on biostars or google in general to see if someone encountered the same problem!

ADD REPLYlink written 2.3 years ago by WouterDeCoster38k
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