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5.1 years ago
n.tear
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80
I'm trying to variant call using VarScan but after sorting the BAM files and creating mpileup files using samtools I get this error using VarScan
Im a novice so any help would be greatly appreciated
java -jar ~/workspace/bioinformaticstools/varscan/varscan-master/VarScan.v2.4.3.jar mpileup2snp /mnt/z/Nathan/WESsamples/unsolved/X366.mpileup >X366.VarScan.snp
Only SNPs will be reported
Warning: No p-value threshold provided, so p-values will not be calculated
Min coverage: 8
Min reads2: 2
Min var freq: 0.2
Min avg qual: 15
P-value thresh: 0.01
Reading input from /mnt/z/Nathan/WESsamples/unsolved/X366.mpileup
Warning: Line ignored: Invalid format for pileup at line 1
╝ �═ BC╗ �╔�B�BCF╝�╗ 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9 MT X Y GL000192.1 GL000225.1 GL000194.1 GL000193.1 GL000200.1 GL000222.1 GL000212.1 GL000195.1 GL000223.1 GL000224. GL000219.1 GL000205.1 GL000215.1 GL000216.1 GL000217.1 GL000199.1 GL000211.1 GL000213.1 GL000220.1 GL000218.1 GL
000209.1 GL000221.1 GL000214.1 GL000228.1 GL000227.1 GL000191.1 GL000208.1 GL000198.1 GL000204.1 GL000233.1 GL000237.1 GL000230.1 GL000242.1 GL000243.1 GL000241.1 GL000236.1 GL000240.1 GL000206.1 GL000232.1 GL000234.1 GL000202.1 GL000238.1 GL000244.1 GL000248.1 GL000196.1 GL000249.1 GL000246.1 GL000203.1 GL000197.1 GL000245.1 GL000247.1 GL000201.1 GL000235.1 GL000239.1 GL000210.1 GL000231. GL000229.1 GL000226.1 GL000207.1 A /mnt/z/NathanHaffordTear/WESsamples/PPCDunsolved/X366.sorted.ba �
GL000219.1 GL000205.1 GL000215.1 GL000216.1 GL000217.1 GL000199.1 GL000211.1 GL000213.1 GL000220.1 GL ##samtoolsVersion=0.1.19-96b5f2294a
The pileup is corrupted. Please post the entire command that was used to generate it. Did you use
nohup
?Hi Thanks for the response. This was the command I used to generate the mpile up file:
I was following instruction from this paper: https://www.biorxiv.org/content/biorxiv/early/2017/10/11/201145.full.pdf
Is that the full command? No
nohup
or anything, or the command embedded in a wrapper function?Yes thats the full command. Sorry im not familiar with nohup or embedding in a wrapper
The thing is that your pileup looks like it was contaminated by some binary information, maybe a mix of
stderr
andstdout
, that is why I was asking. Can you post the output ofI also get this warning when running mpileup with samtools. should I be using bcftools?
I do not know what this is. A mpileup file looks like this:
Do you run this directly via the command line?
okay thanks yes I am running from a ubuntu bash shell on windows. perhaps I need to QC my bam files to check they are correct
Looks like a partial VCF file. Maybe a BCF file?
You should also add the
samtools
command that you used to generate the pileup, because from the error message it seems like the problem lies there.Please use the formatting bar (especially the
code
option) to present your post better. You can use backticks for inline code (`text` becomestext
), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.Hi RamRS. Sorry, will do thanks
I made the changes already :)