Question: CollectAlignmentSummaryMetrics from Picard
0
gravatar for David_emir
21 months ago by
David_emir310
India
David_emir310 wrote:

Hello all,

I have run Picard - CollectAlignmentSummaryMetrics to Produces a summary of alignment metrics on my BAM file. I got a .txt file with columns and rows as follows.

Now i am finding it difficult to interpret these columns. Please help me in understanding these columns, what it signifies and can i get more info on net regarding this?

Column - for categories 1. CATEGORY 2. List item 3. FIRST_OF_PAIR 4.SECOND_OF_PAIR PAIR

and

Columns as follows:

  1. TOTAL_READS
  2. PF_READS
  3. PCT_PF_READS
  4. PF_NOISE_READS
  5. PF_READS_ALIGNED
  6. PCT_PF_READS_ALIGNED
  7. PF_ALIGNED_BASES
  8. PF_HQ_ALIGNED_READS
  9. PF_HQ_ALIGNED_BASES
  10. PF_HQ_ALIGNED_Q20_BASES
  11. PF_HQ_MEDIAN_MISMATCHES
  12. PF_MISMATCH_RATE
  13. PF_HQ_ERROR_RATE
  14. PF_INDEL_RATE
  15. MEAN_READ_LENGTH
  16. READS_ALIGNED_IN_PAIRS
  17. PCT_READS_ALIGNED_IN_PAIRS
  18. BAD_CYCLES
  19. STRAND_BALANCE
  20. PCT_CHIMERAS
  21. PCT_ADAPTER
  22. SAMPLE
  23. LIBRARY
  24. READ_GROUP

Thanks a lot. Dav

ADD COMMENTlink modified 21 months ago by Pierre Lindenbaum116k • written 21 months ago by David_emir310
1

Did you check http://broadinstitute.github.io/picard/picard-metric-definitions.html#AlignmentSummaryMetrics ?

ADD REPLYlink written 21 months ago by Santosh Anand4.6k

Thanks Anand I will go through this.

ADD REPLYlink written 21 months ago by David_emir310
1
gravatar for Pierre Lindenbaum
21 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

see https://broadinstitute.github.io/picard/picard-metric-definitions.html

CATEGORY One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregated for both first and second reads in a pair.

TOTAL_READS The total number of reads including all PF and non-PF reads. When CATEGORY equals PAIR this value will be 2x the number of clusters.

....

ADD COMMENTlink written 21 months ago by Pierre Lindenbaum116k

Thanks a lot for this information, Its really means a lot to me. I will refer this now. Regards, Dav

ADD REPLYlink written 21 months ago by David_emir310
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