only chrM in the varscan2 copynumber output

Question

[lhaiyan3]

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

[WouterDeCoster]

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

[lhaiyan3]

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.

[WouterDeCoster]

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