Filter BAM dataset by CIGAR string "D" (deletion)

Question: Filter BAM dataset by CIGAR string "D" (deletion)

12 months ago by

Hello everyone, I would like to select all reads from a BAM dataset with one deletion, two deletion and so on. I thought to use the CIGAR string putting 1D, 2D and so on depending on the case but when I use the Filter BAM datasets on a variety of attributes tool, I get only those reads with 0 bases and no CIGAR string (apparently all reads). As an example given the two reads below, I get the second one, no matter the filter I use. Does anyone can explain this behavior? Thanks a lot!

M02230:28:000000000-D2Y2R:1:1101:15213:1961 73 chr1 6257782 40 27S87M36S = 6257782 0 CAATCAAGAGTGAACTTCAGAACTT...C AAAAAFFFBFBDEGFFGGGGDGHHHB5B#AAFFGHGGGEGFBFEFGFHHHHBEFA1FGHFHHHHHEF353BFFGED1FCFHBGG4B3@F3F3343FFFHHHGGFFBGGE?///20E/CBHHBFFH322?@G0/02@@CGGCDF?@CCFHF RG:Z:0179 BC:Z:13 SM:i:40 NM:i:3 XN:Z:Coordinate_UserDefined (58174392)_193531064.1 M02230:28:000000000-D2Y2R:1:1101:15213:1961 133 chr1 6257782 0 * = 6257782 0 TGACGTTTCTGGTTCTGTTAANCTTGTTTTNCCGACTGA....

deletions sam galaxy filter bam • 731 views

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modified 12 months ago • written 12 months ago by matteoaccetturo • 0

12 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you don't want to have unmapped reads in the output, also filter for "isMapped" as a second condition.

I don't see any deletions marked in the CIGAR string: 27S87M36S, so this read would not be output if filtering by "nD" (where n == some number of deletion bases).

Help for SAM format: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002/

Hope that helps! Jen, Galaxy team

ADD COMMENT • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k

Sorry I answered, instead of using the reply button. Here is my comment: Thanks Jen, now I get mapped reads, but it seems that the CIGAR filter does not work as I also put 1D to filter on CIGAR string, and I got everything. Here below the parameters I used: Input Parameter Value Note for rerun BAM dataset(s) to filter 1: 0179_S13.bam Select BAM property to filter on cigar Filter on this CIGAR string 1D Select BAM property to filter on isMapped Selected mapped reads True Would you like to set rules? false

Also reads with no deletions or with insertions are present in the output. What mistake do I make?

ADD REPLY • link written 12 months ago by matteoaccetturo • 0

Try this instead using the * to avoid the exact match. This captures other hits you don't want, so filter on MapQ as well. There might be a better way but this works:

Under one Condition use two Filters. Don't use two Conditions or the Filters they contain are applied independently.

cigar set as *nD*
mapQuality set as >0

where *nD* could be *1D*, *2D*... *6D*, etc

ADD REPLY • link modified 12 months ago • written 12 months ago by Jennifer Hillman Jackson ♦ 25k

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