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duncanca / mosaik-aligner

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SNP and indels from SAM #83

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
hi, I use stamtools to deal with SAM form mosaik-aligner to find mutations.
and when i used the command :
samtools pileup -vcf ref.fa aln.bam | tee raw.txt | samtools.pl varFilter -D100 
> flt.txt
awk '($3=="*"&&$6>=50)||($3!="*"&&$6>=20)' flt.txt > final.txt

I got the result whihout any SNP, which is different from other aligner like 
BWA and novoalign.
dsm1731_genome_3940680  70450   *   */-AT   79  79  50  37  *   -AT 36  1   0   0   0
dsm1731_genome_3940680  104757  *   */-ATG  113 113 52  51  *   -ATG    49  2   0   0   0
dsm1731_genome_3940680  347018  *   */-TGC  51  51  51  21  *   -TGC    20  1   0   0   0
dsm1731_genome_3940680  378760  *   */-TTT  54  54  53  20  *   -TTT    19  1   0   0   0
dsm1731_genome_3940680  443907  *   */-TTC  51  51  49  21  *   -TTC    19  2   0   0   0
dsm1731_genome_3940680  570840  *   */-CA   51  51  47  21  *   -CA 19  2   0   0   0
dsm1731_genome_3940680  624467  *   */-C    67  67  51  18  *   -C  15  3   0   0   0
dsm1731_genome_3940680  642655  *   */-AT   63  63  45  17  *   -AT 16  1   0   0   0
dsm1731_genome_3940680  708861  *   */-TA   57  57  54  19  *   -TA 17  2   0   0   0
dsm1731_genome_3940680  739709  *   */-ACC  57  57  52  19  *   -ACC    18  1   0   0   0
dsm1731_genome_3940680  739764  *   */-GT   115 115 48  24  *   -GT 22  2   0   0   0
dsm1731_genome_3940680  828117  *   */-AA   54  54  52  20  *   -AA 19  1   0   0   0

did I make some mistakes? thanks

Original issue reported on code.google.com by guanhui...@gmail.com on 26 Nov 2010 at 10:12

GoogleCodeExporter commented 9 years ago 
Hi,

Did you use "-mm #" parameter of MosaikAligner to allow mismatches?

Best,
Wan-Ping

Original comment by WanPing....@gmail.com on 30 Nov 2010 at 10:12

GoogleCodeExporter commented 9 years ago

Original comment by WanPing....@gmail.com on 30 Nov 2010 at 10:12

GoogleCodeExporter commented 9 years ago 
yes, i use the command following
../bin/MosaikAligner -in sequence_archives/s1_fastq.dat -out 
sequence_archives/s1_fastq_aligned.dat -ia reference/dsm1731_genome.dat -hs 15 
-act 20 -mm 4  -p 16

Original comment by guanhui...@gmail.com on 1 Dec 2010 at 1:55