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Illumina / strelka

Strelka2 germline and somatic small variant caller
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Error in running strelka 2.9.10 #210

Open TZhang11 opened 2 years ago

TZhang11 commented 2 years ago

HI developers,

I'm getting errors while variant calling using the strelka 2.9.10. The error info is shown as follow full_segment_info: key: E00560:276:HHLN3CCX2:8:2222:23084:7233/1 id: 16225 seq: AAAGAAAGGAATCCAAAAAAATGAATTTTTTTTGGATTCCTTTCTTTTACAAATTGTGCTGAGGCAACTATGGCATAGAAATAAACACCATGATACCAGAATCACCATTTCTTTCACATCATCACTCTAGTAAGTTGCATCTAAATATTTT qual: AAFFFJJFFJFJJJJJJJJJJJJJJJJJJJJJJJJJJ7FJJFJJJJJJJJJJJJJFJFJJJJJJJJJFJJJJJJJFAJJJJJJJJJJJJJJJJJJJJAJJFFJJJJJJJJJJJJJJFJFFJAJJJJJJJJJJJFJJFJJJJ-AJFJJFFJF INPUT ALIGNMENT pos: 101023486 strand: F path: 13M65I54N73M is_realigned? 0 buffer_pos: 0 partial_segment 1 : INPUT ALIGNMENT pos: 101023486 strand: F path: 13M65I is_realigned? 0 buffer_pos: 101023486 partial_segment 2 : INPUT ALIGNMENT pos: 101023553 strand: F path: 73M is_realigned? 0 buffer_pos: 101023553

FATAL_ERROR: Exemplar alignment contains indel not found in the overlap indel set Indel: INDEL pos: 101023499 type: INDEL deleteLength: 0 insertSeq: CAAAAAAATGAATTTTTTTTGGATTCCTTTCTTTTACAAATTGTGCTGAGGCAACTATGGCATAG Exemplar overlap set: INDEL pos: 101023500 type: INDEL deleteLength: 0 insertSeq: A status: is_present: 0 is_remove_only: 0

It would be very helpful if you can give some suggestions for this problem. Kind regards, Nicole

Chelseo commented 10 months ago

Hello, I have faced the same question. Did you find the solution?