Varscan Error In Pileup2Snp

Question

[Joel]

I'm trying to use varscan to call snps on exome sequencing. I generated pileups with samtools vs

samtools pileup -f ~/Genomes/hg19/hg19.fa sample1_sorted.bam > sample1.pileup

Then

java -jar VarScan.v2.2.3.jar pileup2snp sample1.pileup --min-var-freq 0.25 --p-value 0.01 > sample1_var.snp

I consistently get an error:

mcmanus@RAMonster:~/Angel_PW_reseqs $ java -jar VarScan.v2.2.3.jar pileup2snp sample4_var.pileup --min-var-freq 0.25 --p-value 0.01 > sample4_var.snp
Min coverage:    8
Min reads2:    2
Min var freq:    0.25
Min avg qual:    15
P-value thresh:    0.01
Reading input from sample4_var.pileup
Input file was not ready after 10 5-second cycles!

Is this file just too long, and can't become "ready" in 10 5-second cycles? How can I work around this?

Answer 1

[Pierre Lindenbaum]

I've tested varscan with an empty file:

>touch tmp.txt
>java -jar VarScan.v2.2.jar pileup2snp tmp.txt --min-var-freq 0.25 --p-value 0.01 
Min coverage:   8
Min reads2: 2
Min var freq:   0.25
Min avg qual:   15
P-value thresh: 0.01
Reading input from tmp.txt
Input file was not ready after 10 5-second cycles!

conclusion: check that your file "sample4_var.pileup" is not empty.

Answer 2

[Dan Koboldt]

Hello,

It could be that the pileup is in an unexpected format (e.g. was generated with the -c or -v parameters). To test your file size issue, do a "head -10" of your pileup file and run VarScan on it.

Yours,

Dan Koboldt

[Joel]

could you please elaborate, how do I do that?

[Joel]

The pileup was not generated with -c or -v parameters. Could u please help me and tell how do I do a "head -10" of the pileup file.

Thanks

[Sean Davis]

head -10 pileupfilename

This assumes a unix-like operating system like Mac OS or Linux.