mpileup failed when using samtools.pl varFilter

[jianfeng.mao]

I used the upper 1000 lines of my sam file to test the pileup process. My mpileup failed, at the second step when using samtools.pl varFilter.

Could you give any directions? I am very new on it. I want to know what has happened? How it can be fixed?

Command_1(here I got a good output):
samtools mpileup -ugf ../01_AL3C3P1-4/Alyrref.folded.fa maplist1000bam-sorted.bam.bam | /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/bcftools/bcftools view -bvcg - > var.raw.bcf

Command_2(here I got error):
/ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/bcftools/bcftools view var.raw.bcf | perl /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl varFilter -D 100 > var.flt.vcf

Error:
Use of uninitialized value in string eq at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 84, <> line 2.
Use of uninitialized value in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 2.
Argument "alt-reverse" isn't numeric in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 3.
Use of uninitialized value in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 4.
Argument "all" isn't numeric in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 5.
Argument "of" isn't numeric in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 6.
Argument "allele" isn't numeric in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 7.
Argument "bias" isn't numeric in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 8.
Use of uninitialized value in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 9.
Use of uninitialized value in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 12.
Use of uninitialized value in string eq at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 84, <> line 13.
Use of uninitialized value in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 13.
Use of uninitialized value in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 14.
Argument "values" isn't numeric in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 15.
Argument "INFO" isn't numeric in numeric lt (<) at /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/misc/samtools.pl line 93, <> line 16.

[jianfeng.mao]

The first step works for me, I checked the "var.raw.bcf".

the commmand:
$ /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/bcftools/bcftools view var.raw.bcf

the output:
##fileformat=VCFv4.0
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability that sample chromosomes are not all the same">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Descriptin="Indicates that the variant is an INDEL.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT map.list1000.bam

[yashumayank]

U are using wrong script I think. Use "vcfutils.pl varFilter" as suggested in the manual of mpileup.