Sam Veiw Output Has * In Seq Column

Question

[mendelson.netta]

Hi,

I have a bam file of aligned sequences (using GEM) which I would like to view. I generated the sam file by running samtools view -h mybam.bam.

Many of the entries in the generated sam file have in their sequence column a * instead of the actual read sequence. For example:

HWI-ST459_116:8:1204:10732:32089#27@0 321 chr10#C2T 63279 9 95M chr16#G2A 32478965 0 * * RG:Z:0.12 NH:i:10 NM:i:3 XT:A:U md:Z:55A10A16A11

However, the same read appears again in the sam file (mapped to a different location) and the sequence there appears correctly:

HWI-ST459_116:8:1204:10732:32089#27@0 65 chr10#C2T 38904960 12 95M chr16#G2A 32478965 0 ATAAATGTTTAAGTTGGTAGTGGAAGATAAAGGATATATAATTTTGGGAGTTTTAGGGTTTTGTTCGTTGTTAGTTTTTTTATGTTATTATAGTT @CCFFFFFHHHHHIIIJAEHHHGHIGIIIJJIJI>FGGGGIJJEHAHIBF8BGGD@GI8BDGGCFEGEG@?A>EEEB@BBB=C:CC>CCADA>@C RG:Z:0.12 NH:i:10 NM:i:5 XT:A:U md:Z:19A46A3G4G7A11

What is the reason for this?

Thanks for the help

Netta

Answer 1

[bow]

The spec (page 4) says that the SEQ column is '*' when the sequence is not stored. I would look into the GEM settings that you use to create the BAM file and see if you've set anything that prevents the reads to be stored there.