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DP in the VCF is different from the number of reads in the bam file after indel realign

LiquanLiquan Beijing, ChinaMember

I have called SNPs and want to use the reads number. However, I found in the VCF file the DP is A(which will be shown in the attached file). However, in the bam file which is used for SNP calling using UnifiedGenotyper, the reads aligned to the specific location is for more larger than A. Can you explain this?
imageimage

Comments

  • valentinvalentin Cambridge, MAMember, Dev ✭✭

    DP is not as simple as the height of the pile-up.

    There are several reasons why a read may not count towards DP... to start I notice that the MQ is rather low (12) so I imagine that many of the reads have relatively low quality at that particular base and that could explain why they are not counted, for example if -mbq is set to something.

    Another possibility is that many of those reads are mark as duplicates (discarded by default).

    Another one for UG is if their mates are mapped to another contig... (an unmapped mate is fine though).

    So it all depends quite a bit as to how you run the program and details in the input data that may not show in a text pile-up

  • MatteodiggMatteodigg ItalyMember

    Hi @valentin and devs,
    I have a problem on DP value between g.vcf and reads reported in IGV before and after haplotypeCaller.
    To be more clear, working on my own script I checked all the position in g.vcf (and final multi-sample vcf too). For example, look at this variant in g.vcf

    chr1 3311101 . C G, 793.77 . BaseQRankSum=1.006;ClippingRankSum=0.000;DP=106;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=381600.00;ReadPosRankSum=-0.933 GT:AD:DP:GQ:PL:SB 0/1:61,42,0:103:99:822,0,1236,1003,1362,2365:29,32,28,14

    Processing bam file I extracted these info corresponding to variant position

    chr1 3311101 C G
    Pair: 115
    Unpair: 0
    Unmapped: 0
    qc_fail: 0
    is_read1: 57
    is_read1_reverse: 29
    is_read1_forward: 28
    is_read2: 58
    is_read2_reverse: 27
    is_read2_forward: 31
    is_reverse: 56
    is_secondary: 1
    is_supplementary: 0
    is_proper_pair_mapped: 112
    Coverage: 115
    mate_is_unmapped: 0
    mean_mapping_qual: 59
    is_unmapped: 0

    So, I found a difference of 12 reads between g.vcf DP and total DP reported on IGV and bam file. When i look at g.vcf.bam (from -bamout option in IGV) I see, instead, a total DP value of 106 (I expected 103 instead).

    My question is, why I see this difference? It depends on Mapping Qual? Unpaired? Both?

    Thank you for your time,

    Matteo

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @Matteodigg
    Hi Matteo,

    I suspect the difference is indeed in the base quality scores. I am a little confused where the coverage of 115 is coming from? Is that from the original BAM file? What about from the bamout file? Notice the DP from the INFO field is 106, but the DP in the FORMAT field is 103. The missing 3 reads are filtered out. Have a look at the documentation for the two annotations here.

    -Sheila

  • MatteodiggMatteodigg ItalyMember

    Hi @Sheila ,
    as I reported before, the bamout file has a DP of 106, like the INFO DP field. The difference between DP in INFO and FORMAT came from 1 read with MAPQ = 1 and (I suppose) the other two reads have been filtered because they are synthetic reads HC 13 and HC 14 (can you confirm that?).
    Yes, the original bam file has a DP of 115. I get these info using pysam and the same DP is reported in other variant callers.
    After that, I intersected the bamout file for variant position with the bamout file from HC to look at reads filtered from HC caller. I know that HC filter some reads to genotype, but I don't understand why some of them have been filtered even if are properly paired, as described in SAM flag (83,163,99,147), and with MQ=60.
    In addition, variant base quality score for each rejected read (except MAPQ 1) is >30. These are all filtered reads:

    M03943:73:000000000-AV81U:1:1108:22334:19322 161 1 3310991 60 151M 2 33141307 151 GAGTGAGGGAGGATGCCCGAGGTCTCACGTCAGGACCCTCGACGGGGGTGGGGTGGAGAGGGAGGTGGTGGGTGGGGTGGGTGGTGCGGCCTGGAGTGGAGCCAAGGGGGGGGCGGCCAGGGTCCACATTGCCCTCTAACGGGACCCCTCG array('B', [31, 31, 31, 31, 35, 33, 37, 36, 32, 31, 29, 32, 33, 33, 38, 38, 36, 37, 32, 34, 38, 36, 32, 37, 36, 38, 36, 37, 32, 33, 37, 35, 37, 37, 32, 37, 36, 36, 38, 37, 32, 33, 36, 32, 36, 36, 36, 36, 32, 38, 36, 36, 36, 27, 34, 36, 34, 38, 34, 34, 35, 36, 32, 34, 35, 31, 38, 36, 30, 38, 36, 35, 27, 33, 35, 35, 36, 27, 33, 36, 36, 27, 33, 36, 30, 38, 37, 30, 35, 38, 36, 36, 34, 38, 34, 39, 31, 38, 33, 34, 38, 37, 32, 36, 35, 39, 34, 36, 36, 36, 35, 35, 35, 36, 32, 35, 36, 29, 34, 37, 35, 34, 30, 35, 32, 30, 36, 34, 32, 32, 38, 36, 34, 35, 35, 35, 35, 32, 33, 36, 32, 33, 35, 30, 31, 34, 34, 33, 32, 32, 28]) [('BD', 'LLNNOPOOLOOOOOPPNKMNNNNNMNNNMMNNPNNNNKNNMNNMMKKKNNNKKNNNNNONNKNNNNNNNNNKNNNKKNNNKNNNNNOMMMNNONNNNNNNNONNKMNKKKKKKMMMMNNPNKNNNNNMOMNONKNNMMLMMMKNNNKKNNM'), ('MD', '5C103C41'), ('PG', 'MarkDuplicates'), ('RG', '20161125_01_Cardio'), ('BI', 'PPRQRRSSORRRRQRRPPQQRRRRQPQPQQRQRQRRQPRPQQRQQNNNRQRNNRQRRRQRRNRRRRQRRQRNRQRNNRQRNRQRRQRQQQPRSRRRQQRRRRPRPQRNNNNNNQQQQPRRRNRRQRPQQPQRPPRPQQNPQQNRRQPPRPQ'), ('NM', 2), ('AS', 141), ('XS', 21)]
    M03943:73:000000000-AV81U:1:1109:23019:7394 401 1 3311088 1 102H48M 1 3311018 48 GGAGCCAAGGGGGGGGCGGCCAGGGTCCACATTGCCCTCTAACGGGAC array('B', [35, 30, 18, 13, 31, 20, 26, 17, 36, 36, 36, 36, 36, 35, 36, 33, 31, 36, 37, 35, 38, 37, 36, 36, 37, 35, 36, 38, 33, 38, 34, 33, 35, 38, 36, 36, 38, 33, 35, 32, 33, 32, 31, 35, 33, 30, 31, 32]) [('SA', 'chr2,33141319,-,42S49M59S,1,0;'), ('BD', 'NNNMNNLNKKKKKKNMMNMNONKNNNNNNONKONLOOPOMNNNLNNLL'), ('MD', '12C35'), ('PG', 'MarkDuplicates'), ('RG', '20161125_01_Cardio'), ('BI', 'QPRQRQPRPPPPPPOPQPQRSRPQRRRQRRQPRQNRRQQRRRRQQRPP'), ('NM', 1), ('AS', 43), ('XS', 19)]
    M03943:73:000000000-AV81U:1:1113:3640:17203 83 1 3311050 60 15S134M 1 3311052 134 TTGGGTAAAAGAGACGGGAGGGGGTGGGGGGGGTGGGTGGTGCGACAAGGAGTGGAGCCAAGGGGGGGGCGGCCAGGATCCACATTGCCCTCTAACGGGACCCCTCGAGAAGCCTCAGCCTCGCCCGCTGACCCTCCTCTCTCCTGCCC array('B', [5, 17, 22, 9, 24, 14, 24, 9, 9, 24, 13, 24, 13, 24, 16, 2, 2, 12, 15, 1, 1, 4, 4, 24, 16, 26, 22, 22, 1, 29, 4, 24, 13, 17, 22, 24, 12, 17, 23, 12, 15, 14, 16, 26, 16, 20, 9, 18, 7, 27, 27, 13, 17, 4, 16, 35, 12, 15, 20, 33, 16, 29, 8, 30, 23, 8, 8, 23, 11, 15, 11, 31, 14, 32, 36, 35, 30, 15, 30, 31, 38, 32, 34, 32, 25, 27, 11, 11, 33, 38, 32, 19, 32, 33, 32, 32, 36, 36, 33, 32, 33, 12, 11, 19, 33, 32, 37, 32, 17, 32, 28, 12, 29, 21, 30, 21, 36, 34, 11, 31, 14, 25, 33, 36, 33, 32, 36, 38, 30, 35, 32, 15, 15, 28, 33, 33, 34, 16, 23, 15, 23, 29, 32, 31, 31, 30, 28, 29, 30]) [('MC', '132M'), ('BD', 'KNKNOLDDLMNMNMMKNNNKKKNNNKKKKKKNNNKNNNNNNMMNNNLNNNNNNNNNMNNLNKKKKKKNMMNMNONNONNNNNONKNMKNNONLMMMKNNNKKNNNMNMNLNMNNOONMNNNMMKMMOPNNNLOOOOOPOPOOOQOMKLL'), ('MD', '6T6T15G1C0T17C11G71'), ('PG', 'MarkDuplicates'), ('RG', '20161125_01_Cardio'), ('BI', 'PRPQQQIIPQPQRQQPQPRPPPQPRPPPPPPQPRPQPRQPRPQRRQPRQPRPRQPRQRQPRPPPPPPPPQPQRSRQQQRRQRRQPRQNRRQQQQQQPQRRNNRRQQPQRPRQRRQSRQRRQQQNQQRRQRRNRRRRRQRRSSSSSQNPP'), ('NM', 7), ('MQ', 60), ('AS', 99), ('XS', 22)]
    M03943:73:000000000-AV81U:1:1114:22354:18380 147 1 3311054 60 23S125M 1 3311048 125 ATGTGTATAAGAAGCAGGCGGGGGGTGGTGGGTGGGTTGGTTGGTGCGGCCTGGAGTGCAGCCAAGGGGCTGGCGGCCAGGCTCCCCATTGCCCTCTAACGGGACCCCTCGAGAAGCCTCAGCCTCGCCCGCTGACCCTCCTCTCTCC array('B', [15, 17, 13, 17, 13, 13, 24, 13, 8, 18, 16, 24, 18, 14, 16, 31, 26, 25, 15, 22, 1, 1, 3, 22, 12, 16, 22, 12, 16, 22, 3, 12, 16, 23, 3, 25, 6, 17, 3, 25, 7, 17, 33, 32, 25, 25, 14, 7, 10, 27, 21, 27, 23, 16, 18, 27, 25, 25, 19, 18, 12, 27, 20, 9, 17, 33, 33, 24, 10, 18, 16, 7, 31, 14, 30, 12, 10, 32, 18, 7, 10, 18, 28, 10, 14, 14, 32, 14, 10, 34, 34, 10, 35, 20, 30, 28, 27, 32, 27, 27, 30, 8, 15, 27, 33, 11, 36, 34, 29, 32, 30, 31, 15, 31, 31, 30, 29, 21, 31, 33, 35, 10, 10, 34, 29, 15, 34, 33, 33, 28, 11, 19, 34, 30, 15, 15, 15, 31, 31, 14, 31, 29, 31, 30, 28, 28, 27, 31]) [('MC', '131M'), ('BD', 'OMNMNLLLLMNLNOONNMMKKKKNNNNNNKNNNKNMKNNMKNNNNMMNMNPNNNNNNOONMNNLNKKNOPNNMMNMNONNONNKKNONKNMKNNONLMMMKNNNKKNNNMNMNLNMNNOONMNNNMMKMMOPOOOLOOOOOPOPNNLL'), ('MD', '13G3G17G11G10G3A62'), ('PG', 'MarkDuplicates'), ('RG', '20161125_01_Cardio'), ('BI', 'QQPQQPQQPQRPRRSRPPQPPPPQPRQPRPQPRPQPPRQPPRQPRPQPQRRRQPRPRRSRQRQPRPPPRRRPPQPQRSRPRRRNNRRQPRQNRRQQQQQQPQRRNNRRQQPQRPQQRRQSRQRRQQQNQQRRQRRNRRRSSRSRRRPP'), ('NM', 6), ('MQ', 60), ('AS', 95), ('XS', 21)]
    M03943:73:000000000-AV81U:1:2112:24719:22353 147 1 3311065 60 150M 1 3310953 150 GGGGGGGGGGTGCGGCCTGGAGGGGAGCCAGGGGGGGGGCGGCCAGGGTCCACATTGCCCTCTAACGGGACCCCTCGAGAAGCCTCAGCCTCGCCCGCTGACCCTCCTCTCTCCTGCCCAGGGCCCGGGACAGGCCACCTGCCCCAGGGG array('B', [25, 24, 2, 2, 26, 32, 26, 22, 26, 26, 24, 12, 15, 29, 14, 24, 20, 17, 29, 24, 17, 22, 3, 32, 24, 17, 13, 5, 16, 24, 1, 36, 35, 36, 35, 36, 33, 33, 30, 25, 36, 37, 38, 38, 38, 36, 36, 36, 32, 37, 38, 34, 38, 34, 33, 33, 38, 35, 37, 38, 34, 38, 32, 34, 33, 32, 36, 36, 31, 27, 36, 35, 36, 34, 34, 32, 37, 35, 37, 34, 37, 38, 36, 38, 34, 38, 37, 37, 36, 38, 33, 32, 37, 36, 36, 32, 37, 38, 36, 37, 32, 36, 36, 38, 34, 36, 38, 33, 38, 35, 38, 33, 36, 38, 36, 37, 36, 37, 38, 37, 36, 35, 38, 36, 36, 32, 36, 37, 37, 32, 39, 36, 37, 38, 36, 38, 32, 36, 35, 33, 34, 34, 34, 34, 33, 34, 31, 31, 33, 31]) [('MC', '151M'), ('BD', 'KKKKKKKKNNNMMNMNPNNNNKKNNNMNONKKKKKKKNMMNMNONKNNNNNNONKNMKNNONLMMMKNNNKKNNNMNMNLNMNNOONMNNNMMKMMOPNNNKNNNNNONONNNPNMKNONKNMKMMKNNNONNMOOOOQONLLOPOKKLL'), ('MD', '3T3T14T7A4C93C16C3'), ('PG', 'MarkDuplicates'), ('RG', '20161125_01_Cardio'), ('BI', 'PPPPPPPPQPRPQPQRRRQPRPPQPRQRSRPPPPPPPPPQPQRSRPQRRRQRRQPRQNRRQQQQQQPQRRNNRRQQPQRPRQRRQSRQRRQQQNQQRRQRRNRRRRRQRQRRRRRQMRSRPPQNQQPQRRSRPQRQRRRRQOOSTSPPPP'), ('NM', 7), ('MQ', 60), ('AS', 118), ('XS', 20)]
    M03943:73:000000000-AV81U:1:2112:13824:17315 147 1 3311069 60 41S110M 1 3311018 110 CGGGGCGGGGGGGGGGGGGAGGGGGGGTGGGGGGGGGGGGGGGGTGGGGCGGCCTGGTGTGGGCCCAAGGGGGGGGCGGCCAGGGTCCACATTGCCCTCTAACGGGACCCCTCGAGAAGCCTCAGCCTCGCCCGCTGACCCTCCTCTCTCC array('B', [24, 2, 2, 2, 13, 15, 35, 32, 26, 22, 1, 1, 22, 35, 35, 29, 29, 22, 14, 14, 30, 1, 30, 22, 22, 22, 13, 15, 1, 1, 1, 1, 26, 22, 1, 1, 32, 29, 1, 26, 1, 32, 29, 26, 16, 22, 24, 1, 12, 14, 4, 13, 5, 26, 16, 26, 12, 16, 12, 25, 1, 4, 12, 27, 24, 20, 9, 17, 7, 36, 32, 26, 23, 7, 7, 10, 25, 36, 36, 35, 38, 31, 32, 30, 37, 33, 35, 38, 31, 39, 34, 33, 35, 37, 36, 37, 38, 30, 38, 32, 34, 32, 32, 36, 36, 37, 32, 36, 36, 36, 38, 33, 32, 37, 37, 35, 34, 36, 37, 36, 38, 33, 38, 36, 34, 33, 31, 31, 31, 36, 36, 37, 32, 39, 38, 34, 35, 32, 35, 32, 32, 34, 27, 32, 31, 32, 33, 32, 30, 32, 31]) [('MC', '150M'), ('BD', 'MKKNMMKKKKKKKKKKKNNNKKKKKNNNKKKKKKKKKKKKKKNNNKKNMMNMNPNNNMNNKNMKNNLNKKKKKKNMMNMNONKNNNNNNONKNMKNNONLMMMKNNNKKNNNMNMNLNMNNOONMNNNMMKMMOPOOOLOOOOOPOPNNLL'), ('MD', '6T9A4A0G8C78'), ('PG', 'MarkDuplicates'), ('RG', '20161125_01_Cardio'), ('BI', 'QPPPPQPPPPPPPPPPPQPRPPPPPQPRPPPPPPPPPPPPPPQPRPPPPQPQRRRQPQPRPPQNRQPRPPPPPPPPQPQRSRPQRRRQRRQPRQNRRQQQQQQPQRRNNRRQQPQRPQQRRQSRQRRQQQNQQRRQRRNRRRSSRSRRRPP'), ('NM', 5), ('MQ', 60), ('AS', 85), ('XS', 19)]
    M03943:73:000000000-AV81U:1:2102:28044:15728 83 1 3311077 60 72S78M 1 3311001 78 CCCAGGGGTCCCCTGCGGGGGCCTGGGGGGGGGGGGGGTTGAGGAGGGGGGGGGGGGGGGGTTGGGGGGGTCCGGCCTGGAGGGGAGCCAGGGGGGGGGCGGCCAGGGTCCACATTGCCCTCTAACGGGACCCCTCGAGAAGCCTCAGCC array('B', [20, 6, 17, 17, 4, 4, 22, 12, 16, 3, 2, 3, 15, 24, 25, 16, 2, 2, 4, 4, 14, 24, 18, 16, 1, 2, 22, 2, 32, 26, 22, 22, 22, 1, 29, 29, 22, 26, 10, 17, 24, 17, 4, 24, 15, 30, 29, 35, 29, 22, 22, 2, 2, 2, 23, 2, 33, 29, 23, 4, 13, 7, 16, 8, 26, 8, 8, 8, 23, 13, 14, 11, 15, 24, 10, 15, 17, 17, 24, 15, 32, 24, 8, 8, 16, 31, 12, 33, 20, 27, 8, 32, 32, 32, 33, 32, 32, 29, 34, 25, 35, 12, 33, 38, 36, 29, 12, 36, 33, 15, 18, 34, 38, 35, 33, 35, 34, 35, 36, 38, 33, 30, 30, 33, 33, 30, 36, 32, 37, 32, 36, 36, 36, 38, 33, 30, 37, 35, 36, 32, 31, 30, 29, 37, 33, 34, 32, 30, 32, 31]) [('MC', '151M'), ('BD', 'KNONLLNNNKKNPNMMKKKNMNPNKKKKKKKKKKKKNMKNNNNNNKKKKKKKKKKKKKKNMKNKKKKKNNNMMNMNPNNNNKKNNNMNONKKKKKKKNMMNMNONKNNNNNNONKNMKNNONLMMMKNNNKKOOONONOMONOOPPNMLL'), ('MD', '10T7A4C54'), ('PG', 'MarkDuplicates'), ('RG', '20161125_01_Cardio'), ('BI', 'NRSRPPQRRNNRRRPQPPPPQRRRPPPPPPPPPPPPQPPQPRQPRPPPPPPPPPPPPPPQPPRPPPPPQRRQQPQRRRQPRPPQPRQRSRPPPPPPPPPQPQRSRPQRRRQRRQPRQNRRQQQQQQPQRRNNRRQQPQRPSRSSRTRQPP'), ('NM', 3), ('MQ', 60), ('AS', 63), ('XS', 20)]
    M03943:73:000000000-AV81U:1:2104:5405:17741 83 1 3311083 60 44S106M 1 3310993 106 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGCCCGGGAGTGGGGCCAGGGGGGGGGCGGCCAGGGTCCACATTGCCCTCTAACGGGACCCCTCGAGAAGCCTCAGCCTCGCCCGCTGACCCTCCTCTCTCCTGCCCAGGGC array('B', [33, 33, 34, 30, 26, 2, 26, 2, 2, 22, 29, 35, 35, 26, 26, 2, 24, 2, 22, 1, 26, 32, 26, 22, 1, 35, 29, 26, 26, 22, 33, 22, 2, 1, 2, 2, 2, 12, 16, 13, 24, 24, 16, 4, 33, 24, 17, 32, 25, 23, 4, 4, 14, 6, 17, 16, 2, 35, 36, 36, 36, 35, 33, 30, 25, 25, 36, 38, 37, 38, 38, 36, 36, 37, 34, 37, 38, 33, 38, 34, 33, 35, 38, 32, 37, 38, 34, 37, 32, 34, 33, 32, 36, 36, 37, 32, 36, 36, 36, 38, 35, 32, 37, 37, 37, 34, 36, 38, 36, 38, 34, 39, 36, 38, 36, 38, 33, 32, 38, 36, 36, 32, 37, 39, 36, 37, 32, 36, 36, 38, 33, 36, 38, 33, 38, 33, 38, 32, 34, 32, 35, 31, 29, 34, 38, 35, 33, 31, 32, 31]) [('SA', 'chr2,33141320,-,38M112S,0,0;'), ('MC', '151M'), ('BD', 'KKKKLLKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKNMMMKMMKNNNNNKKNMNONKKKKKKKNMMNMNONKNNNNNNONKNMKNNONLMMMKNNNKKNNNMNMNLNMNNOONMNNNMMKMMOPNNNKNNNNOPOPOOOQONLOPOKNLL'), ('MD', '7A4A4C88'), ('PG', 'MarkDuplicates'), ('RG', '20161125_01_Cardio'), ('BI', 'PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPQQNQQPQPRPRPPPQRSRPPPPPPPPPQPQRSRPQRRRQRRQPRQNRRQQQQQQPQRRNNRRQQPQRPRQRRQSRQRRQQQNQQRRQRRNRRRRRQRQRRRRSROSTSPPPP'), ('NM', 3), ('MQ', 60), ('AS', 91), ('XS', 0)]
    M03943:73:000000000-AV81U:1:2104:9715:10639 83 1 3311086 60 89S61M 1 3310983 61 GGGGGGTGCCGGGGGTCCACGCGGGGGCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGCCCGGGGGTGGAGCCAGGGGGGGGGCGGCCAGGGTCCACATTGCCCTCTAACGGGACCCCTCGAGAAG array('B', [26, 29, 26, 22, 22, 12, 16, 13, 3, 16, 1, 4, 22, 22, 13, 16, 3, 15, 24, 24, 12, 15, 1, 2, 1, 2, 12, 3, 20, 20, 16, 2, 2, 1, 22, 22, 30, 26, 22, 22, 22, 1, 2, 22, 22, 2, 2, 2, 22, 2, 2, 2, 26, 22, 2, 2, 2, 26, 2, 30, 26, 22, 22, 35, 35, 29, 2, 30, 22, 2, 2, 2, 23, 26, 7, 8, 8, 23, 8, 11, 15, 11, 11, 11, 16, 8, 26, 32, 24, 14, 17, 24, 27, 17, 13, 15, 21, 19, 26, 32, 33, 36, 36, 35, 36, 35, 34, 28, 36, 37, 37, 39, 37, 36, 36, 36, 34, 38, 38, 33, 38, 34, 33, 35, 38, 36, 37, 38, 33, 37, 32, 33, 32, 32, 35, 36, 35, 31, 33, 33, 27, 31, 34, 30, 35, 33, 31, 28, 32, 31]) [('SA', 'chr2,33141319,-,30S50M70S,0,0;'), ('MC', '151M'), ('BD', 'KKKKOONMMMKKKNNNNNMMMMKKKNMKKMMKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKNMMMKMMKKKNNNNNNMNONKKKKKKKNMMNMNONKNNNNNNONKNMKNNONLMNNLOOOLLOOONONNLLL'), ('MD', '9A4C46'), ('PG', 'MarkDuplicates'), ('RG', '20161125_01_Cardio'), ('BI', 'PPPPQPRQQQPPPQRRRQQQPQPPPPQNNQQPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPQQNQQPPPQPRQPRQRSRPPPPPPPPPQPQRSRPQRRRQRRQPRQNRRQQQQQQPQRRNNSSRRQRRPPP'), ('NM', 2), ('MQ', 60), ('AS', 51), ('XS', 19)]
    M03943:73:000000000-AV81U:1:1105:18756:9300 147 1 3311088 60 77S73M 1 3310971 73 GGTCGCGGTCAGGGCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCGGGGGGGGAGCCAGGGGGGGGGCGGCCAGGGTCCACATTGCCCTCTAACGGGACCCCTCGAGAAGCCTCAGCCTCGCCC array('B', [22, 12, 15, 24, 12, 15, 8, 13, 14, 16, 16, 26, 22, 12, 2, 20, 24, 1, 1, 26, 1, 1, 30, 35, 35, 33, 22, 1, 29, 35, 35, 30, 24, 1, 22, 1, 1, 29, 33, 35, 30, 26, 22, 32, 26, 1, 26, 24, 1, 35, 26, 1, 2, 35, 35, 30, 26, 1, 29, 24, 1, 24, 22, 1, 1, 1, 1, 26, 12, 24, 14, 7, 33, 26, 7, 7, 7, 35, 16, 16, 12, 27, 19, 17, 7, 35, 36, 35, 36, 36, 36, 32, 29, 32, 36, 37, 37, 38, 37, 36, 36, 37, 34, 37, 38, 33, 38, 34, 33, 35, 38, 36, 38, 38, 34, 37, 32, 34, 33, 32, 36, 36, 37, 32, 36, 36, 36, 38, 33, 32, 38, 36, 38, 33, 36, 38, 36, 38, 34, 38, 34, 34, 34, 35, 32, 32, 32, 31, 33, 32]) [('SA', 'chr2,33141339,-,17S75M58S,0,4;'), ('MC', '151M'), ('BD', 'NNNMMMNNOONKNMKMMKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKNMMMKKKKKKNNNMNONKKKKKKKNMMNMNONKNNNNNNONKNMKNNONLMMMKNNNKKNNNMNMNLONOOPPONOOONMKLL'), ('MD', '7A4C60'), ('PG', 'MarkDuplicates'), ('RG', '20161125_01_Cardio'), ('BI', 'QRQQPQQRQSRPPQNQQPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPQQQPPPPPPQPRQRSRPPPPPPPPPQPQRSRPQRRRQRRQPRQNRRQQPQQQPQRRNNRRQQPQRPRQRRQSRRSSRRQNPP'), ('NM', 2), ('MQ', 60), ('AS', 63), ('XS', 19)]
    M03943:73:000000000-AV81U:1:1109:23019:7394 97 1 3311018 60 118M 2 33141318 118 CGTCAGGACCCTCGACGGGGGTGGGGTGGAGAGGGAGGTGGTGGGTGGGGTGGGTGGTGCGGCCTGGAGTGGAGCCAAGGGGGGGGCGGCCAGGGTCCACATTGCCCTCTAACGGGAC array('B', [31, 29, 29, 32, 34, 35, 35, 34, 33, 34, 34, 36, 36, 32, 33, 36, 32, 36, 36, 36, 36, 32, 38, 36, 36, 36, 30, 34, 33, 33, 38, 34, 38, 36, 36, 33, 38, 36, 27, 37, 36, 27, 38, 35, 36, 27, 34, 36, 36, 35, 32, 38, 36, 36, 31, 38, 36, 32, 38, 37, 31, 36, 38, 36, 36, 38, 35, 33, 38, 32, 38, 36, 34, 38, 36, 36, 36, 33, 38, 36, 36, 36, 36, 35, 35, 35, 36, 31, 35, 36, 34, 33, 37, 35, 35, 32, 35, 35, 34, 36, 34, 32, 32, 38, 36, 35, 35, 35, 35, 35, 32, 33, 36, 32, 35, 35, 33, 36]) [('BD', 'LLMNOQOOOOLOONOONNKKKNNNKKNNNNNONNKNNNNNNNNNKNNNKKNNNKNNNNNOMMMNNONNNNNNNNONNKMNKKKKKKMMMMNNPNKNNNNNMOMNONKNNMMLMMMKNN'), ('MD', '82C35'), ('PG', 'MarkDuplicates'), ('RG', '20161125_01_Cardio'), ('BI', 'PPQRRSSSSRPRPQQRQQNNNRQRNNRQRRRQRRNRRRRQRRQRNRQRNNRQRNRQRRQRQQQPRSRRRQQRRRRPRPQRNNNNNNQQQQPRRRNRRQRPQQPQRPPRPQQNPQQNRR'), ('NM', 1), ('AS', 113), ('XS', 21)]

    I'm trying to understand why they have been filtered. Right now, I'm running HC again by disabling all filters.
    Thank you for your help,

    Matteo

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @Matteodigg
    Hi Matteo.

    I think the flag I referred you to in the other thread will help.

    -Sheila

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