Filter bam files using a bed file: Why is the mate missing?

Question

[komal.rathi]

Hi everyone,

This is a sorted bam (by coordinates):

samtools view 7316-161-T_Aligned.out.sorted.bam | grep 'FCC78FRACXX:1:1101:6639:75204'

FCC78FRACXX:1:1101:6639:75204#  163 chr2    74156623    255 23M2445N77M =   74159237    8677    CGCCTATCAATCAGATTAAACTCCTGAACAAAGAAAATAAAGTGCTTAAAGGAGGTGTTGAGGTGGGCCTCCTCTTGCAGCTGCATCACAGAATCAAAGT    bbbeeeeegggggiiiiihiiiihhiihiiiihiihiifhf]Yafaccfggfcgh^ceghhhi_ceghggggeeceedddcbccbccccc_bbcccc`c]    NH:i:1  HI:i:1  AS:i:199    NM:i:0  MD:Z:100

FCC78FRACXX:1:1101:6639:75204#  83  chr2    74159237    255 18M5963N82M =   74156623    -8677   TTTTGGGAAATGGGACACCAATCTTAGAAGGAAAAAGAGTTTCATCATCAAGCTGATCTTGAACCCAAGTCATCAAATAGTCAATGTATTTTGGTGCAGA    ^cccddddb`deeeedbbdggggagiiihiiihhiiiiihhhgchihhiihhhhhfiihihfciieiiiiihhiehihiiihiiiiigggggeeeeebbb    NH:i:1  HI:i:1  AS:i:199    NM:i:0  MD:Z:100

I filtered out the reads mapped to a particular region like this:

head genes_10000Flanks.bed
chr2    74109441        74156992        ACTG2

samtools view -b -L genes_10000Flanks.bed 7316-161-T_Aligned.out.sorted.bam -o 7316-161-T_Aligned.out.filtered_new.bam

But when I look at the filtered bam file I only get one mate:

samtools view 7316-161-T_Aligned.out.filtered_new.bam | grep 'FCC78FRACXX:1:1101:6639:75204'

FCC78FRACXX:1:1101:6639:75204#  163 chr2    74156623    255 23M2445N77M =   74159237    8677    CGCCTATCAATCAGATTAAACTCCTGAACAAAGAAAATAAAGTGCTTAAAGGAGGTGTTGAGGTGGGCCTCCTCTTGCAGCTGCATCACAGAATCAAAGT    bbbeeeeegggggiiiiihiiiihhiihiiiihiihiifhf]Yafaccfggfcgh^ceghhhi_ceghggggeeceedddcbccbccccc_bbcccc`c]    NH:i:1  HI:i:1  AS:i:199    NM:i:0  MD:Z:100

Why is the other mate not getting filtered?

Answer 1

[Pierre Lindenbaum]

because the position 74159237 is out of the segment 74109441-74156992 and the L option doesn't work as you expect. If you want to retrieve all the reads, extends your bed or add a second step to retrieve all the reads by name. https://www.google.com/search?q=site%3Abiostars.org+read+names+bam

[komal.rathi]

Thanks I just thought it would be simpler than this. I was hoping something like a partial match would work..