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Old 03-19-2013, 06:22 AM   #1
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Location: NY

Join Date: Apr 2011
Posts: 9
Default snp calling with samtools

hi all,
i am a new for snp calling with samtools in transcriptome data. recently, i am trying to call snps with samtools. I set the option as follows:
samtools mpileup -B -ugSD -f ref.fa aln_sorted.bam | bcftools view -Nbcvg - > aa.bcf
i use the default that samtools manual lists.but i think i need set the option,especially for -D(such as -D100), according to my data, but i don't know the rules or criterion clearly. i think the -D is difficult to set because the data is from RNA-seq. so i am not dry behind the ears for this.
can you help me, dear? thx~
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Old 03-19-2013, 09:19 AM   #2
Location: Vancouver, BC

Join Date: Dec 2012
Posts: 30

samtools mpileup -C50 -l location_list -d 1000000 -L 1000000 -AEfu ref.fasta my.bam > result.vcf
This is how I run mpileup on rna-seq. The large numbers for -d and -L are due to very high coverage regions is RNA seq experiments. We didn't want it to ignore high coverage regions, so we set them very high. The -l list is because I only wanted calls for certain locations. -E is extended BAQ computation... don't understand much about that but apparent;y its a good idea. -C50 is recommended for bwa alignments. -u is for getting the output as an uncompressed vcf.
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Old 03-26-2013, 05:51 PM   #3
Location: Nanjing, China

Join Date: Mar 2013
Posts: 10

Hi, all,
I got a document from , it says using pileup file from samtools and junctions.bed file generated by tophat with bedtools to filter SNPs, how do you think?
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