Samtools Mpileup Doesn'T Show Deletion, When Deletion Between Paddings

Question

[tsk]

Given the following sam file, containing six reads, with all reads having a deletion in the same position in the end of the reads.

The mpileup does not show the '-1' in the position, but correctly inputs '*" on the next reference position. Is this a minor bug in samtools when the neighbouring CIGARs are paddings?

samtools view -h tmpError.bam

SQ    SN:ref_contig    LN:17050216
@PG    ID:DSA_APP
vic_10_05f-8292314    0    ref_contig    368    255    17M1P12M1P10M1P23M5P7M4P16M1P4M1P1D1P1M1P2M    *    0    0    TCCACCTTAGACACAAGTTTGTTTCGACTCTCAGTGACATTTTGCCGAGAAATATTGGGGGAGCCGGTATATACAGCATCACCTGTACTATC    GG@GGGGGGHGHHHHHHHHHHFHHHHHHHGEGGGFBGGBHHHHHHHHHHHHHDHHHHHHCECAA-AE?EGGDGGHHHHHHGHGHHEHEEEGG
vic_10_05f-15094200    0    ref_contig    368    255    17M1P12M1P10M1P23M5P7M4P16M1P4M1P1D1P1M1P2M    *    0    0    TCCACCTTAGACACAAGTTCGTTTCGACTCTCAGTGACATTTTGCCGAGAAATATTGGGGGAGCCGGTATATACAGCATCACCTGTACTATC    IIIHIIIIHIIIIGHGIIIHIIIIIHIHIHHGGIFIDIHIIIIHIIIIIHIIIGIIHIIIIHIFIHIDHIHGIIIHHHHIIHHHIFGGIHHB
vic_10_05f-21262821    0    ref_contig    368    255    17M1P12M1P10M1P23M5P7M4P16M1P4M1P1D1P1M1P2M    *    0    0    TCCACCTTAGACACAAGTTTGTTTCGACTCTCAGTGACATTTTGCCGAGAAATATTGGGGGAGCCGGTATATACAGCATCACCTGTACTATC    IIIIIIIIIIIIGHIFIIIIIHGIIIHIIIEIBIEIBGEIIII<GIHHIEIIIHHIHGIIIGH=IIG@BIIHHGHGIHIGGGFGE@DFEDC8
vic_10_05f-13951224    0    ref_contig    368    255    17M1P12M1P10M1P23M5P7M4P16M1P4M1P1D1P1M1P2M    *    0    0    TTCACCTTAGACACAAGTTCGTTTCGACTCTCAGTGACATTTTGCCGAGAAATATTGGGGGAGCCGGTATATACAGCATCACCTGTACTATC    HHHHHHHHHHHHHDHHHHHGHHHHHHHHHHHHBGDHHHBHHHHEHHHHHDHHHHHHEHHHHBHHHHHGHHHHHHHHHDHHGHHFHBHHDHGG
vic_10_05f-7803303    0    ref_contig    368    255    17M1P12M1P10M1P23M5P7M4P16M1P4M1P1D1P1M1P2M    *    0    0    TCCACCTTAGACACAAGTTCGTTTCGACTCTCAGTGACATTTTGCCGAGAAATATTGGGGGAGCCGGTATAGACCACATCACCTGTACTATC    IIIIIIIIGHIHIIIIHFIIIHIIIIDIIIHIEGBGGGDIIIIIIIIEIEDGGEHIIIHIIHIIIGFEIGIIGFEDIBHHIHHDIEFBIFHB
vic_10_05f-28850663    0    ref_contig    368    255    17M1P12M1P10M1P23M5P7M4P16M1P4M1P1D1P1M1P2M    *    0    0    TCCACCTTAGACACAAGTTTGTTTCGACTCTCAGTGACATTTTGCCGAGAAATATTGGGGGAGCCGGTATATACAGCATCACCTGTACTATC    HHHHHHHHHHHGHGGDGEGGDFFFHHHHEHHHDHGHFHBHHHHHHHHGHBEEHEHHEGGGHEECGGHDEGECGCEBGGGDGDFDD?DDAABE

samtools mpileup tmpErr.bam |tail

[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
ref_contig    451    N    6    TTTTTT    HHGFDD
ref_contig    452    N    6    GGGGGG    HIEHID
ref_contig    453    N    6    TTTTTT    EF@BE?
ref_contig    454    N    6    AAAAAA    HGDHFD
ref_contig    455    N    6    CCCCCC    EGFHBD
ref_contig    456    N    6    TTTTTT    EIEDIA // <- should show '-1'
ref_contig    457    N    6    ******    EHDHFA // <- corrrect here
ref_contig    458    N    6    AAAAAA    EHDHFA
ref_contig    459    N    6    TTTTTT    GHCGHB
ref_contig    460    N    6    C$C$C$C$C$C$    GB8GBE

samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd

Thanks

Answer 1

[aroob.lab]

Hello, I have the same issue. did you find a solution ?

Thanks