Question: Samtools Mpileup Doesn'T Show Deletion, When Deletion Between Paddings
1
gravatar for tsk
6.0 years ago by
tsk10
tsk10 wrote:

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

ngs bam samtools mpileup • 1.7k views
ADD COMMENTlink written 6.0 years ago by tsk10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1601 users visited in the last hour