Samtool Pileup output format

Question

[Prasad]

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

[Devon Ryan]

Why are you using a version of samtools from 2009? You're not going to get any help for such an old version.

[Prasad]

In the latest version mpileup is there. i couldnot understand which options to select for this kind of output. any comments on columns

[Devon Ryan]

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.

[Martombo]

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.

[Prasad]

thanks a lot