Question: Samtool Pileup output format
0
gravatar for Prasad
4.9 years ago by
Prasad1.6k
India
Prasad1.6k wrote:

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

 

samtools • 2.3k views
ADD COMMENTlink written 4.9 years ago by Prasad1.6k

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

ADD REPLYlink written 4.9 years ago by Devon Ryan92k

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

ADD REPLYlink written 4.9 years ago by Prasad1.6k
2

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.

ADD REPLYlink written 4.9 years ago by Devon Ryan92k

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.

ADD REPLYlink written 4.9 years ago by Martombo2.6k

thanks a lot

ADD REPLYlink written 4.9 years ago by Prasad1.6k
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