Bug Report For Samtools View

[Tlexander]

Dear All,

Recently, I find a bug for samtools view. you can input chr:start-end in samtools view, also you can take bed file ( -L bed file) to appoint interest region. But you will find they will get different result.

if you use the latter method (-L bed file), you will get lots of result from non-interest region.


Is there anyone also come cross such promblems. If you have some solulation, please tell me [email protected]. Thanks





HS7_194:4:2202:2133:117418 83 2 219461081 60 75M = 219460994 -162 CCCTTATTTTGTGTTTTCCATCCCTCTCCCTTAACAGGATTGAAATAAAACATGCTTCTGTTTTTGTAAAAAAAA DDCDDDDDDDDCEFFFEFHGFIIJJJGHGHJIJ
HS7_194:4:2305:2063:197273 147 2 219461081 60 75M = 219461019 -137 CCCTTATTTTGTGTTTTCCATCCCTCTCCCTTAACAGGATTGAAATAAAACATGCTTCTGTTTTTGTAAAAATAA FFFFHHHEEIIIFIGECGHHAHGFAHHIIGDBH
HS7_194:4:1102:18963:133633 99 2 219461125 60 75M = 219461219 169 ATAAAACATGCTTCTGTTTTTGTAAAAATAATTTTTCCTTTACACTGGAGATTTTATTCTATCAGTATATGGGTA @@@FFFFFHGGGHIGG@?FGGIEDDHGIGIIIG
HS7_194:4:1105:13468:65364 1699 2 219461125 60 75M = 219461217 169 ATAAAACATGCTTCTGTTTTTGTAAAAATAATTTTTCCTTTACACTGGAGATTTTATTCTATCAGTATATGGGTA =???DDB?A2::BF<@AEIHJ?HIJEHCEFHCG
HS7_194:4:1101:1015:2212 589 * 0 0 * * 0 0 GNAAATGAGAACAGGAAACTTCCATCTGAGCCCTGAGGATGGGCATGGTTTCCAGGTCCTCTTCCTGCTTTGCAA #################################################
HS7_194:4:1101:1015:2212 653 * 0 0 * * 0 0 TGGCAGAGNNNNNTCTGGCTTCCAANNANCNNCAAATGGATGAAATGAAGCAAACCATAGCCAAGCAGGAAGCAC +1===+=:#####+2+2AF;3CF+*##)#1##))00)9?DB?DB<B###
HS7_194:4:1101:1015:24338 589 * 0 0 * * 0 0 GNATCTGGATCTACCTATATCTATATGTGAGCATACATATATAATATATACACACAGATACAAGTGTACACACAC #################################################
HS7_194:4:1101:1015:24338 653 * 0 0 * * 0 0 GTATCATAGCCATGACTGACTT

[dpryan]

Do the "non-interesting" reads span over your region of interest? That's the most likely cause. It would also be nice if you could post a reproducible example.