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  • nilshomer
    replied
    Originally posted by bioinfosm View Post
    When the flag field is '*', does it mean an unmapped read? I know that a flag 4 is definitely unmapped.
    The '*' in the flag field is invalid, and does not conform to the specification (see the "Note" in Section 2.2.1).

    Leave a comment:


  • bioinfosm
    replied
    When the flag field is '*', does it mean an unmapped read? I know that a flag 4 is definitely unmapped.

    Leave a comment:


  • nilshomer
    replied
    Originally posted by rcorbett View Post
    Hi all,
    I have a bam file created from illumina alignments with bwa. When I try to get the number of aligned reads 2 different ways I get 2 different numbers...

    When I run flagstat:
    samtools flagstat myBam.bam
    I get this many mapped reads
    41721001 mapped (93.82%)

    However when I try to get this on my own with this command:
    samtools view myBam.bam | awk -F '\t' '($3 != "*")' | wc -l
    I get this number
    42283661

    I'm sure I'm doing something wrong, but not sure what. Is it incorrect to think that all reads with a non '*' listed in the third column should be considered aligned?

    thanks for the help!
    You want:
    Code:
    samtools view -f 4 myBam.bam | wc -l
    See the FLAG field in the SAM spec.

    Leave a comment:


  • rcorbett
    started a topic samtools flagstat mismatch in stats

    samtools flagstat mismatch in stats

    Hi all,
    I have a bam file created from illumina alignments with bwa. When I try to get the number of aligned reads 2 different ways I get 2 different numbers...

    When I run flagstat:
    samtools flagstat myBam.bam
    I get this many mapped reads
    41721001 mapped (93.82%)

    However when I try to get this on my own with this command:
    samtools view myBam.bam | awk -F '\t' '($3 != "*")' | wc -l
    I get this number
    42283661

    I'm sure I'm doing something wrong, but not sure what. Is it incorrect to think that all reads with a non '*' listed in the third column should be considered aligned?

    thanks for the help!

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