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.
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.
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