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  • Flagstat vs. Picard AlignmentSummaryMetrics

    Hi everyone,

    I am having a bit of trouble making ends meet with this two tools.
    I have a whole genome realigned with GATK and am trying to get the alignment stats to report. I tried samtools and picard only to find different numbers reported:

    Total Reads:

    picard: 1206005136
    samtools: 1209724136
    dif: 3719000

    This same difference is also found in the mapped/aligned totals. The percentages aligned are the same (99.7). Also, Picard shows exact numbers
    I guess there is some difference in the way the programs handle flags.
    Also, I tried removing the duplicates with both programs, samtools and picard, but no methot equated the numbers. More so, flagstat reported duplicates after RMDUP (but not after picard filter reads).

    Does anyone know why this is happening and what can I do to equate the summaries, or how to choose between both?

    Thanks in advance for all the help.

    PS, These are the numbers:

    Flagstat:

    1209724136 + 0 in total (QC-passed reads + QC-failed reads)
    146098358 + 0 duplicates
    1206039846 + 0 mapped (99.70%:-nan%)
    1209724136 + 0 paired in sequencing
    604530215 + 0 read1
    605193921 + 0 read2
    1172988734 + 0 properly paired (96.96%:-nan%)
    1203916910 + 0 with itself and mate mapped
    2122936 + 0 singletons (0.18%:-nan%)
    23043913 + 0 with mate mapped to a different chr
    11749717 + 0 with mate mapped to a different chr (mapQ>=5)

    PICARD – METRICS..............................
    ..............................
    CATEGORY..............................FIRST_OF_PAIR..........SECOND_OF_PAIR..........PAIR
    TOTAL_READS..............................603002568..........603002568..........1206005136
    PF_READS..............................603002568..........603002568..........1206005136
    PCT_PF_READS..............................1....................1....................1
    PF_NOISE_READS..............................0....................0....................0
    PF_READS_ALIGNED....................601970451..........600350395..........1202320846
    PCT_PF_READS_ALIGNED....................0.998288..........0.995602..........0.996945
    PF_ALIGNED_BASES....................60151224632..........59727879851..........119879104483
    PF_HQ_ALIGNED_READS....................561713306..........559548407..........1121261713
    PF_HQ_ALIGNED_BASES....................56471172468..........56055351192..........112526523660
    PF_HQ_ALIGNED_Q20_BASES....................55582307306..........54668254292..........110250561598
    PF_HQ_MEDIAN_MISMATCHES....................0....................0....................0
    PF_MISMATCH_RATE....................0.00499....................0.005764..........0.005376
    PF_HQ_ERROR_RATE....................0.003378..........0.004162..........0.003768
    PF_INDEL_RATE..............................0.000263..........0.000259..........0.000261
    MEAN_READ_LENGTH....................101..........101..........101
    READS_ALIGNED_IN_PAIRS....................600149693..........600149693..........1200299386
    PCT_READS_ALIGNED_IN_PAIRS..........0.996975..........0.999666..........0.998319
    BAD_CYCLES..............................0..........0..........0
    STRAND_BALANCE..............................0.500892..........0.500784..........0.500838
    PCT_CHIMERAS..............................0.019654..........0.019654..........0.019654
    PCT_ADAPTER..............................0.000048..........0.000024..........0.000036
    SAMPLE..............................
    LIBRARY..............................
    READ_GROUP..............................

  • #2
    I've run into this today also, so would be interested to hear what causes the difference:

    Without listing all the stats, an example is the number of properly paired reads reported by FlagStat:

    13990908 + 0 properly paired (94.85%:-nan%)

    Compared to Picard:

    PCT_READS_ALIGNED_IN_PAIRS
    FIRST_OF_PAIR 0.992012
    SECOND_OF_PAIR 0.995876
    PAIR 0.99394

    Comment


    • #3
      Originally posted by gibberwocky View Post
      I've run into this today also, so would be interested to hear what causes the difference:

      Without listing all the stats, an example is the number of properly paired reads reported by FlagStat:

      13990908 + 0 properly paired (94.85%:-nan%)

      Compared to Picard:

      PCT_READS_ALIGNED_IN_PAIRS
      FIRST_OF_PAIR 0.992012
      SECOND_OF_PAIR 0.995876
      PAIR 0.99394


      Thanks sir for more information you provide here
      Help me a lot
      http://watchfree.me/10/w.png

      Comment


      • #4
        Hi Sinemi,
        I am having the same issue and I was wondering if you ever worked this out?

        Comment


        • #5
          Hi sinemi and gibberwocky,
          I am having the same issue and I was wondering if you resolved this issue?

          Comment

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