CollectAlignmentSummaryMetrics from Picard

Question

[David_emir]

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

[Santosh Anand]

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

[David_emir]

Thanks Anand I will go through this.

Answer 1

[Pierre Lindenbaum]

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.

....

[David_emir]

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