Question: a problem with varscan
gravatar for ZoeChing
15 months ago by
ZoeChing0 wrote:

hi there. I have been using VarScan to call for de novo mutation in varscan . And an error occured in the trio calling step which i didn't figure out how to fix it.


$samtools mpileup -B -q 1 -f $ref_dir/ucsc.hg19.fasta $bam_dir/SZ_295B.dedupped.realigned.recal.bam $bam_dir/SZ_295C.dedupped.realigned.recal.bam $bam_dir/SZ_295A.dedupped.realigned.recal.bam > SZ295.mpileup java -jar $varscan trio SZ295.mpileup SZ295.mpileup.output \ --min-coverage 10 \ --min-var-freq 0.20 \ --p-value 0.1 \ -adj-var-freq 0.05 \ -adj-p-value 0.15


SNPs will be output to SZ295.mpileup.output.snp.vcf

Indels will be output to SZ295.mpileup.output.indel.vcf

Min coverage: 10

Min reads2: 4

Min var freq: 0.2

Min avg qual: 15

P-value thresh: 0.1

Adj. min reads2: 2

Adj. var freq: 0.05

Adj. p-value: 0.15

Reading input from SZ295.mpileup

Parsing Exception on line:

chr1 10181 a 4 .,G. <bbb 2="" .,="" bw="" 0="" <="" p="">



java.lang.ArrayIndexOutOfBoundsException: 10

    at net.sf.varscan.Trio.<init>(

    at net.sf.varscan.VarScan.trio(

    at net.sf.varscan.VarScan.main(

Varscan have generated two vcf file as output only contains the genomic positions before "chr1 10181". So, after some checking on the mpileup file, i found it was empty on the row of "chr1 10181", column 11. I thought that may be the cause of this error until i realized that this row is not the first one which is emty on column 11. Before "chr1 10181", there were five genomic positions empty on column 11 and none of them was presented in the output vcf files.

Is there anybody have experienced this error? How can i fix it?

Any suggestion will be greatly appreciated.


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