Hi,
I'm beginner of varScan. I'm using Varscan.v2.3.2 to do SNPs calling. Here is what I did according to the on line manual.(I’m using samtool 0.1.18)
samtools mpileup -d8000 -f ./hg19.fa ./mybam.bam | java -jar ./VarScan.v2.3.2.jar mpileup2snp --output-vcf 1 >my.mpileup2snp.vcf
In the result vcf file, there are all “N” in the column 4 (REF column).. Here is the example part of output by “less -S my.mpileup2snp.vcf” command
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
1 131249 . N G . PASS ADP=8;WT=0;HET=
1 131250 . N G . PASS ADP=8;WT=0;HET=
1 131251 . N C . PASS ADP=8;WT=0;HET=
1 131252 . N C . PASS ADP=9;WT=0;HET=
1 131253 . N C . PASS ADP=9;WT=0;HET=
1 131254 . N A . PASS ADP=8;WT=0;HET=
1 131255 . N G . PASS ADP=9;WT=0;HET=
1 131256 . N C . PASS ADP=8;WT=0;HET=
1 131257 . N A . PASS ADP=9;WT=0;HET=
Anything I did was wrong? Would you please help?
Thank you,
Xin
I'm beginner of varScan. I'm using Varscan.v2.3.2 to do SNPs calling. Here is what I did according to the on line manual.(I’m using samtool 0.1.18)
samtools mpileup -d8000 -f ./hg19.fa ./mybam.bam | java -jar ./VarScan.v2.3.2.jar mpileup2snp --output-vcf 1 >my.mpileup2snp.vcf
In the result vcf file, there are all “N” in the column 4 (REF column).. Here is the example part of output by “less -S my.mpileup2snp.vcf” command
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
1 131249 . N G . PASS ADP=8;WT=0;HET=
1 131250 . N G . PASS ADP=8;WT=0;HET=
1 131251 . N C . PASS ADP=8;WT=0;HET=
1 131252 . N C . PASS ADP=9;WT=0;HET=
1 131253 . N C . PASS ADP=9;WT=0;HET=
1 131254 . N A . PASS ADP=8;WT=0;HET=
1 131255 . N G . PASS ADP=9;WT=0;HET=
1 131256 . N C . PASS ADP=8;WT=0;HET=
1 131257 . N A . PASS ADP=9;WT=0;HET=
Anything I did was wrong? Would you please help?
Thank you,
Xin
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