Entering edit mode
7.3 years ago
lhaiyan3
▴
80
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
Duplicate of ChrM in the Varscan2 copynumber output
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
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.
Good, next time first try searching on biostars or google in general to see if someone encountered the same problem!