Samtool Pileup output format
Hi all,
/samtools-0.1.7a/samtools pileup -cf NC_006834_oryzae.fasta bam_output_sorted.bam >pileup
This is the sample output
NC_006834_X_oryzae_KACC10331 19 A G 30 30 60 1 ^~g I
NC_006834_X_oryzae_KACC10331 20 G A 30 30 60 1 a I
NC_006834_X_oryzae_KACC10331 21 C T 30 30 60 1 t I
NC_006834_X_oryzae_KACC10331 22 C C 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 23 A A 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 24 G G 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 25 C C 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 26 A A 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 27 A A 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 28 C C 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 29 A A 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 30 G G 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 31 A A 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 32 T T 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 33 G G 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 34 A A 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 35 T T 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 36 C C 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 37 A A 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 38 T T 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 39 A A 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 40 C C 30 0 60 1 , I
NC_006834_X_oryzae_KACC10331 41 T T 30 0 60 1 ,$ I
NC_006834_X_oryzae_KACC10331 42 T G 30 30 60 1 ^~g I
NC_006834_X_oryzae_KACC10331 43 T A 30 30 60 1 a I
NC_006834_X_oryzae_KACC10331 44 G R 7 7 60 2 a^~. II
NC_006834_X_oryzae_KACC10331 45 A A 33 0 60 2 ,. II
I got the information for first 6 column from the manual. but the remaining columns I could not understand. Where can I get the strand and read depth info. what are those 7-10 columns
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Why are you using a version of samtools from 2009? You're not going to get any help for such an old version.
In the latest version mpileup is there. i couldnot understand which options to select for this kind of output. any comments on columns
In such an old version, no, who knows what sort of bugs it had in its output. The current version of samtools still has the mpileup command (the -c option hasn't existed in a while, I have no idea what that does) and I get the standard 6 columns with it.
you can still get a similar pileup with the latest version of samtools, have a look here. the last three columns of your output are, probably, the same as the last three of the latest format described in the link, that is: number of reads at position, info about reads (orientation, mismatches, start/end) and quality.
thanks a lot