Picard CollectAlignmentMetrics Output

Question

[fiona.newberry]

I am confused by the output that Picard CollectAlignmentMetrics is giving me. I think it is the format.

## METRICS CLASS    picard.analysis.AlignmentSummaryMetrics
CATEGORY    TOTAL_READS PF_READS    PCT_PF_READS    PF_NOISE_READS  PF_READS_ALIGNED    PCT_PF_READS_ALIGNED    PF_ALIGNED_BASES    PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE    PF_HQ_ERROR_RATE    PF_INDEL_RATE   MEAN_READ_LENGTH    READS_ALIGNED_IN_PAIRS  PCT_READS_ALIGNED_IN_PAIRS  BAD_CYCLES  STRAND_BALANCE  PCT_CHIMERAS    PCT_ADAPTER SAMPLE  LIBRARY READ_GROUP
FIRST_OF_PAIR   1000000 1000000 1   0   1000000 1   99990119    999271  99917232    99487798    0   0.003925    0.003924    0.00009100  1000000 1   0   0.50084 0   0           
SECOND_OF_PAIR  1000000 1000000 1   0   1000000 1   99989751    999225  99912264    99481794    0   0.003919    0.003919    0.00009100  1000000 1   0   0.49916 0   0           
PAIR    2000000 2000000 1   0   2000000 1   199979870   1998496 199829496   198969592   0   0.003922    0.003922    0.000092    100 2000000 1   0   0.5 0   0

Is there a way to format this so that it is readable?

Thanks

[WouterDeCoster]

You can add formatting by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

I'm not sure how the output should look like so I haven't changed your post.

Answer 1

[Pierre Lindenbaum]

using awk:

 curl -Ls "https://raw.githubusercontent.com/ewels/MultiQC_TestData/master/data/modules/picard/CollectMultipleMetrics/A1.sorted.dup.recal.all.metrics.alignment_summary_metrics" |\
awk '/^CATEGORY/ {split($0,header);n=1;next; } {if(n!=1) next; for(i=2;i<=NF;++i) printf("%s\t%s\t%s\n",$1,header[i],$i);}' |\
column -t

.

FIRST_OF_PAIR   TOTAL_READS                 48300305
FIRST_OF_PAIR   PF_READS                    48300305
FIRST_OF_PAIR   PCT_PF_READS                1
FIRST_OF_PAIR   PF_NOISE_READS              0
FIRST_OF_PAIR   PF_READS_ALIGNED            48290537
FIRST_OF_PAIR   PCT_PF_READS_ALIGNED        0.999798
FIRST_OF_PAIR   PF_ALIGNED_BASES            6040566328
FIRST_OF_PAIR   PF_HQ_ALIGNED_READS         47217927
FIRST_OF_PAIR   PF_HQ_ALIGNED_BASES         5910135054
FIRST_OF_PAIR   PF_HQ_ALIGNED_Q20_BASES     5804787451
FIRST_OF_PAIR   PF_HQ_MEDIAN_MISMATCHES     0
FIRST_OF_PAIR   PF_MISMATCH_RATE            0.00187
FIRST_OF_PAIR   PF_HQ_ERROR_RATE            0.001761
FIRST_OF_PAIR   PF_INDEL_RATE               0.000093
FIRST_OF_PAIR   MEAN_READ_LENGTH            125.537288
FIRST_OF_PAIR   READS_ALIGNED_IN_PAIRS      48246679
FIRST_OF_PAIR   PCT_READS_ALIGNED_IN_PAIRS  0.999092
FIRST_OF_PAIR   BAD_CYCLES                  0
FIRST_OF_PAIR   STRAND_BALANCE              0.44083
FIRST_OF_PAIR   PCT_CHIMERAS                0.001303
FIRST_OF_PAIR   PCT_ADAPTER                 0.000001
SECOND_OF_PAIR  TOTAL_READS                 48300305
SECOND_OF_PAIR  PF_READS                    48300305
SECOND_OF_PAIR  PCT_PF_READS                1
SECOND_OF_PAIR  PF_NOISE_READS              0
SECOND_OF_PAIR  PF_READS_ALIGNED            48250591
SECOND_OF_PAIR  PCT_PF_READS_ALIGNED        0.998971
SECOND_OF_PAIR  PF_ALIGNED_BASES            6025327891
SECOND_OF_PAIR  PF_HQ_ALIGNED_READS         47170746
SECOND_OF_PAIR  PF_HQ_ALIGNED_BASES         5894822755
SECOND_OF_PAIR  PF_HQ_ALIGNED_Q20_BASES     5697735258
SECOND_OF_PAIR  PF_HQ_MEDIAN_MISMATCHES     0
SECOND_OF_PAIR  PF_MISMATCH_RATE            0.002515
SECOND_OF_PAIR  PF_HQ_ERROR_RATE            0.002401
SECOND_OF_PAIR  PF_INDEL_RATE               0.000097
SECOND_OF_PAIR  MEAN_READ_LENGTH            125.429941
SECOND_OF_PAIR  READS_ALIGNED_IN_PAIRS      48246679
SECOND_OF_PAIR  PCT_READS_ALIGNED_IN_PAIRS  0.999919
SECOND_OF_PAIR  BAD_CYCLES                  0
SECOND_OF_PAIR  STRAND_BALANCE              0.559123
SECOND_OF_PAIR  PCT_CHIMERAS                0.001303
SECOND_OF_PAIR  PCT_ADAPTER                 0.000001
PAIR            TOTAL_READS                 96600610
PAIR            PF_READS                    96600610
PAIR            PCT_PF_READS                1
PAIR            PF_NOISE_READS              0
PAIR            PF_READS_ALIGNED            96541128
PAIR            PCT_PF_READS_ALIGNED        0.999384
PAIR            PF_ALIGNED_BASES            12065894219
PAIR            PF_HQ_ALIGNED_READS         94388673
PAIR            PF_HQ_ALIGNED_BASES         11804957809
PAIR            PF_HQ_ALIGNED_Q20_BASES     11502522709
PAIR            PF_HQ_MEDIAN_MISMATCHES     0
PAIR            PF_MISMATCH_RATE            0.002192
PAIR            PF_HQ_ERROR_RATE            0.002081
PAIR            PF_INDEL_RATE               0.000095
PAIR            MEAN_READ_LENGTH            125.483615
PAIR            READS_ALIGNED_IN_PAIRS      96493358
PAIR            PCT_READS_ALIGNED_IN_PAIRS  0.999505
PAIR            BAD_CYCLES                  0
PAIR            STRAND_BALANCE              0.499952
PAIR            PCT_CHIMERAS                0.001303
PAIR            PCT_ADAPTER                 0.000001

[fiona.newberry]

Thank you. What does the curl do at the beginning of your code?

[WouterDeCoster]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

[Pierre Lindenbaum]

curl just gets a summary file i've found on the web

[fiona.newberry]

Sorry to ask another question, but I am confused as to how actually use the above command. I am new to linux. My filename is metrics.txt so would i put that at the end of the awk command?

[Pierre Lindenbaum]

o would i put that at the end of the awk command

yes or just 'cat'

cat your.file.metrics |\
awk '/^CATEGORY/ {split($0,header);n=1;next; } {if(n!=1) next; for(i=2;i<=NF;++i) printf("%s\t%s\t%s\n",$1,header[i],$i);}'  |\
column -t

[fiona.newberry]

Another question. It does not recognise the column -t section

[Pierre Lindenbaum]

Strange.. column is quite common.

but your can jyst remove the 'column -t' part. It's just here to reformat the text; or install 'column' https://unix.stackexchange.com/questions/330506/

[fiona.newberry]

Thanks, it seems to be working now. Is there a way to change the format in the actual text file? Not the version printed to the terminal