Dear all,
Old version of samtools snp calling works fine but with 1.1 version I get no
ref in column, please see below. Any ideas what has gone wrong or is it a bug?
* bwa index NC_010079.fasta
* bwa mem -M -t 60 NC_010079.fasta frag_1.fastq frag_2.fastq >
FadyTest.sam
* /home/data/rking/samtools-1.1/bin/bin/samtools view -b FadyTest.sam >
FadyTest.bam
* /home/data/rking/samtools-1.1/bin/bin/samtools sort -O bam -T rob
FadyTest.bam > FadyTestsort.bam
* samtools mpileup -ugf NC_010079.fasta FadyTestsort.bam | bcftools view
-bvcg - > var.raw.bcf
* bcftools view var.raw.bcf |
/home/data/andyp_bioinf/tools/samtools-0.1.19/bcftools/vcfutils.pl varFilter
-D 100 > var.flt.vcf
output
* #CHROM POS ID REF ALT
QUAL FILTER INFO FORMAT FadyTestsort.bam
* NC_010079 1 . T A
116 .
DP=14;VDB=6.844596e-04;AF1=1;AC1=2;DP4=0,0,8,0;MQ=60;FQ=-51 GT:PL:GQ
1/1:149,24,0:45
* NC_010079 2 . A C
116 .
DP=14;VDB=1.047483e-03;AF1=1;AC1=2;DP4=0,0,7,1;MQ=60;FQ=-51 GT:PL:GQ
1/1:149,24,0:45
* NC_010079 3 . C T
140 .
DP=14;VDB=4.352398e-04;AF1=1;AC1=2;DP4=0,0,9,1;MQ=60;FQ=-57 GT:PL:GQ
1/1:173,30,0:57
* NC_010079 4 . T A
107 .
DP=15;VDB=2.322963e-03;AF1=1;AC1=2;DP4=0,0,8,0;MQ=60;FQ=-51 GT:PL:GQ
1/1:140,24,0:45
* NC_010079 5 . G C
174 .
DP=15;VDB=9.674624e-04;AF1=1;AC1=2;DP4=0,0,7,3;MQ=60;FQ=-57 GT:PL:GQ
1/1:207,30,0:57
* /home/data/rking/samtools-1.1/bin/bin/samtools mpileup -uv -f
NC_010079.fasta FadtTestsort.bam > testFadyNewsam.vcf
output
* NC_010079 71 . C <X> 0 .
DP=17;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0PL 0,0,0
* NC_010079 72 . A <X> 0 .
DP=17;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0PL 0,0,0
* NC_010079 73 . T <X> 0 .
DP=17;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0PL 0,0,0
* NC_010079 74 . C <X> 0 .
DP=17;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0PL 0,0,0
* NC_010079 75 . A <X> 0 .
DP=17;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0PL 0,0,0
--
This message has been scanned for viruses and
dangerous content by MailScanner, and we believe
but do not warrant that this e-mail and any attachments
thereto do not contain any viruses. However, you are fully
responsible for performing any virus scanning.
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
