Bedtools bamToBed paired end problems

[sgoodwin]

I have generated artificial sequences with Sherman and aligned them using bwa. I then used samtools to sort the read and generate a bam file.

The file is sorted by name as required by the bamToBed -bedpe option.

bedToBam -bedpe -i myFile.bam > myFile.bed

When I run this I get this error for every single read

*****WARNING: Query 6390_chr10:91632437-91632600_R1 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.

Here is a sample of my input for reference:

4_chr2:183066786-183066895_R1 83 chr2 183066795 60 101M = 183066787 -109 AGTCATAATTCCTAAATATTATTATTTTTAATCTGAAAGGAACTTTAGCCATTTTAAAGAAAAACTATTCCAAATACAGTATTATATAGTATTTCAATGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:101
4_chr2:183066786-183066895_R2 163 chr2 183066787 60 101M = 183066795 109 TCTTCTGCAGTCATAATTCCTAAATATTATTATTTTTAATCTGAAAGGAACTTTAGCCATTTTAAAGAAAAACTATTCCAAATACAGTATTATATAGTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:101

here is a sample of my header:

@HD VN:1.3 SO:queryname
@SQ SN:chrM LN:16571
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260




I have tried adding a /1 or /2 to the end of the name but no luck. Any thoughts?

[sgoodwin]

solution

I figured it out.

In case anyone has the same problem as me - bedTools expects that the QNAME field is idnetical for the pair.