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
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
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